M6389
|
Echis C-type lectin DNA alignment |
|
Nucleic Acid |
130 |
519 |
|
|
|
M12530
|
Tetrapod |
|
Nucleic Acid |
9 |
20791 |
|
|
|
M16260
|
Reptile Mitochondrial sequences |
|
Amino Acid |
28 |
11214 |
|
|
|
M4201
|
RAG1 |
Legacy TreeBASE Matrix ID = M4602 |
Nucleic Acid |
52 |
1368 |
|
|
|
M25073
|
Plant AGOs |
MSA of plant AGOs |
Amino Acid |
270 |
621 |
|
|
|
M23443
|
Neomys ALAD intron 10 |
|
Nucleic Acid |
14 |
644 |
|
|
|
M3436
|
Final Riboprotein Alignment |
Legacy TreeBASE Matrix ID = M3463 |
Amino Acid |
38 |
11428 |
|
|
|
M10275
|
abv2 |
1st and 2nd codon positions of the three genes |
Nucleic Acid |
50 |
3421 |
|
|
|
M44789
|
Entorrhiza within Fungi AA |
|
Amino Acid |
58 |
729 |
|
|
|
M47830
|
Hominid Primates 1sample group2 filtered |
|
Nucleic Acid |
6 |
1000 |
|
|
|
M3168
|
Nuclear Dataset |
Legacy TreeBASE Matrix ID = M3830 |
Nucleic Acid |
133 |
1520 |
|
|
|
M7131
|
48Taxa_8685_bin8_recode |
based on the amino acid sequences of 78 ribosomal proteins recoded using 8 minmax chi-squared bins |
Unspecified |
48 |
8685 |
|
|
|
M21788
|
Tryptophan 2,3-Dioxygenase Alignment |
|
Amino Acid |
98 |
357 |
|
|
|
M5501
|
part 02 |
|
Nucleic Acid |
233 |
33840 |
|
|
|
M3059
|
ADRAB AR GHR VWF Tenrecs |
Legacy TreeBASE Matrix ID = M3679 |
Nucleic Acid |
38 |
5439 |
|
|
|
M17423
|
COI 197 items Rodentia 20130221 |
|
|
197 |
645 |
|
|
|
M3807
|
Class V chitinases, Fig. 4 |
Legacy TreeBASE Matrix ID = M4075 |
Amino Acid |
83 |
605 |
|
|
|
M25498
|
Histone chaperone CAF1A matrix |
|
Nucleic Acid |
10 |
1894 |
|
|
|
M16619
|
arrestins |
arrestins |
Amino Acid |
29 |
391 |
|
|
|
M38906
|
Thiolase alignment |
Protein sequence alignment for differentially located thiolases |
Amino Acid |
24 |
471 |
|
|
|
M44979
|
Multiprotein-bridging factor 1 (MBF1) |
|
Amino Acid |
39 |
122 |
|
|
|
M8381
|
Nuclear rhodopsin anura matrice |
DNA 1 gene |
Nucleic Acid |
20 |
282 |
|
|
|
M30391
|
Diatom cyclin-dependent kinase A2 CDK alignment MUSCLE |
|
Nucleic Acid |
60 |
226 |
|
|
|
M11012
|
full dataset |
|
Amino Acid |
55 |
11500 |
|
|
|
M25497
|
Histone chaperone ASF1 matrix |
|
Nucleic Acid |
22 |
481 |
|
|
|
M15950
|
test NO30 no32 iTOL 94seq |
|
Unspecified |
94 |
14359 |
|
|
|
M5509
|
part 10 |
|
Nucleic Acid |
233 |
42229 |
|
|
|
M30076
|
Eukaryotic root filtered ALPHA-PROT dataset |
|
Amino Acid |
77 |
9261 |
|
|
|
M19425
|
Piwi-Argonaute |
|
Amino Acid |
28 |
512 |
|
|
|
M47833
|
Hominid Primates 1 sample group3 filtered |
|
Nucleic Acid |
6 |
1000 |
|
|
|
M5381
|
Fig. 2 Character Matrix |
|
Nucleic Acid |
413 |
3632 |
|
|
|
M2858
|
EF-1a |
Legacy TreeBASE Matrix ID = M2079 |
Nucleic Acid |
47 |
2330 |
|
|
|
M21616
|
S Blocks |
unmasked proteins of the small ribosomal subunit |
Amino Acid |
25 |
17924 |
|
|
|
M21792
|
3-Hydroxyanthranilate-3,4-Dioxygenase Alignment |
|
Amino Acid |
136 |
263 |
|
|
|
M19426
|
Vasa-PL10 |
|
Amino Acid |
26 |
370 |
|
|
|
M5380
|
Fig. 1B Character Matrix |
|
Nucleic Acid |
60 |
3045 |
|
|
|
M40964
|
Holothuroidea Reduced Dataset Matrix |
|
Nucleic Acid |
84 |
4296 |
|
|
|
M30079
|
Eukaryotic root filtered EUBAC dataset |
|
Nucleic Acid |
80 |
9555 |
|
|
|
M43499
|
Dicer mafft_coredomains |
|
Amino Acid |
1229 |
1375 |
|
|
|
M987
|
IRBP ADRA2B vWF |
Legacy TreeBASE Matrix ID = M2481 |
Nucleic Acid |
62 |
3768 |
|
|
|
M33142
|
Protista Aminoacid Matrix |
Concatenated alignment |
Amino Acid |
73 |
113208 |
|
|
|
M16283
|
alignment gammatype |
|
Amino Acid |
46 |
149 |
|
|
|
M25074
|
Plant and Animal AGOs |
MSA of plant and animal AGOs |
Amino Acid |
302 |
521 |
|
|
|
M3066
|
Metazoa RPL-RPS |
Legacy TreeBASE Matrix ID = M3686 |
Amino Acid |
32 |
9377 |
|
|
|
M21786
|
Nicotinate-Nucleotide Adenylyltransferase Alignment |
|
Amino Acid |
134 |
322 |
|
|
|
M11030
|
Primates |
|
Nucleic Acid |
191 |
34941 |
|
|
|
M34085
|
Birds Clocklike Exons |
first and second codon position of 1156 clock-like exons for 48 species from Jarvis et al (2014, Science 346), which we filtered for missing data (positions with missing data or gaps for any taxa were deleted) resulting in a final alignment of 124,196 bases. |
Nucleic Acid |
48 |
124196 |
|
|
|
M16273
|
All types ML |
|
Amino Acid |
179 |
107 |
|
|
|
M22746
|
NASP TPR4 |
TPR4 sequences |
Amino Acid |
52 |
34 |
|
|
|
M4856
|
mtDNA for ranids |
Legacy TreeBASE Matrix ID = M4940 |
Amino Acid |
39 |
3280 |
|
|
|
M14518
|
MCM5 + MCM8 metazoans MCM domain alignment |
Alignment of MCM domain of MCM5 and MCM8 |
Amino Acid |
25 |
720 |
|
|
|
M1117
|
GSKnt |
Legacy TreeBASE Matrix ID = M2623 |
Nucleic Acid |
139 |
1044 |
|
|
|
M8584
|
SSU |
492 taxon SSU alignment with all characters |
Nucleic Acid |
492 |
9398 |
|
|
|
M15198
|
Matrix Partition 1 |
|
Nucleic Acid |
10 |
750000 |
|
|
|
M21764
|
mouse data Matrix |
|
Nucleic Acid |
8 |
279 |
|
|
|
M46752
|
Isopentenyltransferase genes PfamIPPT seed |
PfamIPPT seed alignment |
Amino Acid |
1246 |
846 |
|
|
|
M3023
|
HBB-T1 |
Legacy TreeBASE Matrix ID = M3624 |
Nucleic Acid |
4 |
1427 |
|
|
|
M1972
|
EF-1alpha |
Legacy TreeBASE Matrix ID = M3326 |
Nucleic Acid |
27 |
716 |
|
|
|
M36816
|
Tursiops truncatus 7A al TRAV |
|
Nucleic Acid |
90 |
385 |
|
|
|
M2351
|
actin |
Legacy TreeBASE Matrix ID = M925 |
Nucleic Acid |
41 |
893 |
|
|
|
M8164
|
Alb3 |
|
Nucleic Acid |
17 |
1204 |
|
|
|
M9470
|
5 genes dataset untrimmed |
untrimmed alignment of 4 protein codeing genes and SSU rRNA gene |
Combination |
70 |
6654 |
|
|
|
M7125
|
42Taxa_11544AA |
based on 11,544 amino acid positions derived from 78 ribosomal proteins of 42 taxa |
Amino Acid |
42 |
11544 |
|
|
|
M7135
|
48Taxa_5710AA |
based on 5,710 amino acid positions derived from the 39 ribosomal proteins with the least heterogeneity |
Unspecified |
48 |
5710 |
|
|
|
M19791
|
Mammal Catsper3-intron-5 |
|
Nucleic Acid |
15 |
303 |
|
|
|
M3696
|
SSU rDNA |
Legacy TreeBASE Matrix ID = M824 |
Nucleic Acid |
48 |
1878 |
|
|
|
M8088
|
TR1 |
|
Nucleic Acid |
17 |
906 |
|
|
|
M4860
|
Riboprotein super-alignment, 62 Taxa |
Legacy TreeBASE Matrix ID = M4937 |
Amino Acid |
62 |
11544 |
|
|
|
M21790
|
Kynurenine-3-Monooxygenase Alignment |
|
Amino Acid |
114 |
421 |
|
|
|
M15203
|
Matrix Partition 4 |
|
Nucleic Acid |
10 |
750000 |
|
|
|
M23454
|
Neomys SLA intron 2 |
|
Nucleic Acid |
14 |
813 |
|
|
|
M21973
|
Murinae CO1 |
|
Nucleic Acid |
244 |
645 |
|
|
|
M2244
|
12S 18 taxa |
Legacy TreeBASE Matrix ID = M625 |
Nucleic Acid |
18 |
2616 |
|
|
|
M25499
|
Histone chaperone CAF1B Matrix |
|
Nucleic Acid |
12 |
1146 |
|
|
|
M30375
|
Plethodontidae 38taxa_50NPCLs_Karsenia_koreana_excluded |
38taxa_50NPCLs_Karsenia_koreana_excluded |
Nucleic Acid |
37 |
48582 |
|
|
|
M6380
|
Echis C-type lectin amino acid alignment |
Echis C-type lectin |
Amino Acid |
116 |
173 |
|
|
|
M10952
|
IRBP cytB TR ND2 |
|
Nucleic Acid |
31 |
4454 |
|
|
|
M17422
|
Cytb 425items Glires |
|
|
425 |
1107 |
|
|
|
M3165
|
Table 1 |
Legacy TreeBASE Matrix ID = M3827 |
Nucleic Acid |
56 |
7995 |
|
|
|
M22753
|
NASP Coding sequence Full |
NASP coding sequences |
Nucleic Acid |
43 |
2883 |
|
|
|
M61770
|
Rattus Sundaland 27x11339 |
|
Nucleic Acid |
27 |
11339 |
|
|
|
M18376
|
AQP3.nexus |
|
Nucleic Acid |
29 |
768 |
|
|
|
M22744
|
NASP TPR3 |
TPR3 sequences |
Amino Acid |
52 |
34 |
|
|
|
M3027
|
HBB spacer 2 |
Legacy TreeBASE Matrix ID = M3628 |
Nucleic Acid |
5 |
15000 |
|
|
|
M57723
|
Ochropsora |
|
|
21 |
552 |
|
|
|
M38300
|
Glycoside hydrolases family 20 Protein Alignment |
Sequence alignement used to infer Figure 1 |
Amino Acid |
69 |
443 |
|
|
|
M36141
|
Pyruvate Transporter TaBASS2 |
nexus file of TaBASS2 |
Amino Acid |
42 |
529 |
|
|
|
M1513
|
Globins |
Legacy TreeBASE Matrix ID = M2363 |
Amino Acid |
38 |
251 |
|
|
|
M23455
|
Neomys TRAIP intron 8 |
|
Nucleic Acid |
14 |
617 |
|
|
|
M126
|
Eukaryotic EF-1alpha |
Legacy TreeBASE Matrix ID = M1500 |
Amino Acid |
27 |
269 |
|
|
|
M3026
|
HBB-T2 |
Legacy TreeBASE Matrix ID = M3627 |
Nucleic Acid |
4 |
1401 |
|
|
|
M47836
|
Hominid Primates 2 samples group2 unfiltered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M1366
|
Caudata Nuclear rRNA |
Legacy TreeBASE Matrix ID = M2153 |
Nucleic Acid |
26 |
2819 |
|
|
|
M38415
|
Raith et al COI MESQ |
|
Nucleic Acid |
808 |
1693 |
|
|
|
M7126
|
36Taxa_11544AA |
based on 11,544 amino acid positions derived from 78 ribosomal proteins of 36 taxa |
Amino Acid |
36 |
11544 |
|
|
|
M3028
|
HBB spacer 1 |
Legacy TreeBASE Matrix ID = M3629 |
Nucleic Acid |
5 |
15000 |
|
|
|
M11730
|
MPEG1-perforin-C6 |
MPEG1-perforin-C6 alignment |
Amino Acid |
12 |
269 |
|
|
|
M17421
|
COI 75 items Lagomorpha |
|
|
75 |
645 |
|
|
|
M16620
|
GRK |
G protein receptor kinase |
Amino Acid |
19 |
629 |
|
|
|
M326
|
LSU-SSU rRNA |
Legacy TreeBASE Matrix ID = M1162 |
Secondary Chemistry |
29 |
1540 |
|
|
|
M43498
|
Dicer muscle_coredomains |
|
Amino Acid |
1229 |
1633 |
|
|
|
M32452
|
Folate metabolism-related genes in maize SHMT1 |
|
Amino Acid |
10 |
681 |
|
|
|
M35274
|
Metazoan Bcl2 |
|
Amino Acid |
78 |
104 |
|
|
|
M5510
|
SOS |
|
Amino Acid |
117 |
37476 |
|
|
|
M16259
|
Mammalian Mitochondrial sequences |
|
Amino Acid |
68 |
3658 |
|
|
|
M3543
|
Muroid supermatrix |
Legacy TreeBASE Matrix ID = M4035 |
Nucleic Acid |
21 |
3777 |
|
|
|
M2926
|
ALDH |
Legacy TreeBASE Matrix ID = M3497 |
Amino Acid |
105 |
899 |
|
|
|
M23445
|
Neomys CSF2 intron 2 |
|
Nucleic Acid |
14 |
734 |
|
|
|
M8085
|
SRY |
|
Nucleic Acid |
17 |
786 |
|
|
|
M1457
|
AP5 extended taxon set |
Legacy TreeBASE Matrix ID = M2267 |
Nucleic Acid |
66 |
475 |
|
|
|
M12529
|
Amniote |
|
Nucleic Acid |
7 |
94251 |
|
|
|
M43507
|
Dicer muscle-gb |
|
Amino Acid |
1255 |
911 |
|
|
|
M44788
|
Entorrhiza within Fungi DNA |
|
Nucleic Acid |
58 |
2918 |
|
|
|
M35838
|
Microtubule associated protein Tau |
|
Amino Acid |
102 |
1953 |
|
|
|
M46115
|
Human Genotypes |
|
Nucleic Acid |
173 |
6 |
|
|
|
M30078
|
Eukaryotic root full EUBAC dataset |
|
Nucleic Acid |
80 |
10055 |
|
|
|
M206
|
18S |
Legacy TreeBASE Matrix ID = M1029 |
Nucleic Acid |
78 |
2555 |
|
|
|
M36864
|
Ascomycota, concatenated protein coding alignment |
concatenated protein coding alignment |
Amino Acid |
33 |
38945 |
|
|
|
M48582
|
Alignment of ODAM protein-coding exons |
RAxML analysis |
Nucleic Acid |
165 |
1177 |
|
|
|
M47837
|
Hominid Primates 2 samples group3 unfiltered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M47839
|
Hominid Primates 2 samples group3 filtered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M257
|
Pteropus |
Legacy TreeBASE Matrix ID = M1086 |
Matrix Representation |
58 |
22 |
|
|
|
M18372
|
AGT.nexus |
|
Nucleic Acid |
30 |
972 |
|
|
|
M10610
|
CEA receptor in human and dog |
|
Nucleic Acid |
9 |
816 |
|
|
|
M8176
|
Echis phospholipase A2 DNA alignment |
|
Nucleic Acid |
42 |
444 |
|
|
|
M23448
|
Neomys GDAP1 intron 1 |
|
Nucleic Acid |
14 |
689 |
|
|
|
M37814
|
ABCA transporters phylogeny of eight species |
|
Nucleic Acid |
78 |
8512 |
|
|
|
M5504
|
part 05 |
|
Nucleic Acid |
233 |
31840 |
|
|
|
M16234
|
PRP8 exteins |
|
Amino Acid |
46 |
1921 |
|
|
|
M2447
|
vWF (intron 11) |
Legacy TreeBASE Matrix ID = M1807 |
Nucleic Acid |
31 |
901 |
|
|
|
M154
|
GHR BRCA1 RAG1 c-myc nuDNA |
Legacy TreeBASE Matrix ID = M1780 |
Nucleic Acid |
64 |
6399 |
|
|
|
M16124
|
Homo sapiens from southern Africa |
The matrix contain sequences of unique haplotypes used in the study. These haplotypes were used to generate the likelihood tree in TreeBase and Figure S3 in the manuscript and the Network in the manuscript (Figure 2). Each haplotype may represent many different individuals. A haplotype list with number of individuals and group classification is available online (http://wiredspace.wits.ac.za/bitstream/handle/10539/8992/CM_SCHLEBUSCH_THESIS.pdf) in Appendix E |
Nucleic Acid |
247 |
1131 |
|
|
|
M36819
|
Tursiops truncatus 7B al TRDV |
|
Nucleic Acid |
45 |
417 |
|
|
|
M43364
|
Dicer elision |
|
Amino Acid |
1255 |
37320 |
|
|
|
M41466
|
900-species Muroidea, 6 nuclear and 1 mitochondrial loci |
900-species Muroidea, 6 nuclear and 1 mitochondrial loci |
Nucleic Acid |
913 |
8831 |
|
|
|
M24362
|
Cetacea Alignment Type I Keratins |
|
Nucleic Acid |
221 |
3493 |
|
|
|
M11422
|
Phylogenomic Metazoa |
|
|
51 |
53799 |
|
|
|
M8461
|
10 16 Sub 90 protein |
Amino acid section of concatenaed dataset |
Amino Acid |
89 |
5699 |
|
|
|
M20995
|
Metazoan CDK |
|
Amino Acid |
76 |
283 |
|
|
|
M18375
|
AQP2.nexus |
|
Nucleic Acid |
27 |
606 |
|
|
|
M5676
|
SSU 16AA all taxa |
|
Amino Acid |
451 |
6578 |
|
|
|
M8090
|
vWF11 |
|
Nucleic Acid |
17 |
938 |
|
|
|
M2320
|
Appendix 3 |
Legacy TreeBASE Matrix ID = M888 |
Morphological |
68 |
186 |
|
|
|
M6391
|
Echis phospholipase A2 amino acid alignment |
|
Amino Acid |
33 |
144 |
|
|
|
M45575
|
Character Matrix figure S1A tree |
Comparison of p120 sequences |
Amino Acid |
17 |
250 |
|
|
|
M46500
|
Rotifer 90 glutathione S-transferase |
|
Nucleic Acid |
133 |
231 |
|
|
|
M8092
|
ZFYLI |
|
Nucleic Acid |
17 |
714 |
|
|
|
M25506
|
Histone chaperone SSRP matrix |
|
Nucleic Acid |
9 |
819 |
|
|
|
M15202
|
Matrix Partition 3 |
|
Nucleic Acid |
10 |
750000 |
|
|
|
M19861
|
Euglenida MATMATX |
alignment |
Amino Acid |
123 |
638 |
|
|
|
M44206
|
Rana MHCII exon3 |
|
Nucleic Acid |
51 |
291 |
|
|
|
M21814
|
S1 proteases family |
|
Amino Acid |
75 |
397 |
|
|
|
M608
|
Eukaryotic eRF3 |
Legacy TreeBASE Matrix ID = M1507 |
Amino Acid |
17 |
269 |
|
|
|
M8084
|
SMCY11 |
|
Nucleic Acid |
17 |
618 |
|
|
|
M37815
|
ABCB full transporters phylogeny of eight species |
|
Nucleic Acid |
42 |
3203 |
|
|
|
M43468
|
Dicer elision-gb |
|
Amino Acid |
1255 |
3220 |
|
|
|
M23501
|
Prd/Pitx transcription factor gene superfamily alignment |
Fig E6 |
Amino Acid |
164 |
64 |
|
|
|
M21204
|
African Galagids 27 loci complete |
Matrix including 27 loci |
Nucleic Acid |
30 |
18248 |
|
|
|
M20936
|
Muroid Rodents Concatenated nuDNA: BRCA1, GHR, IRBP, RAG1 |
|
Nucleic Acid |
305 |
6720 |
|
|
|
M10276
|
a2bv2 |
1st 2nd codon positions of VWF and ADRA2B plus all codon positions of BRCA1 |
Nucleic Acid |
50 |
4350 |
|
|
|
M47840
|
Hominid Primates 3 samples filtered |
|
Nucleic Acid |
16 |
1000 |
|
|
|
M22742
|
NASP TPR1 |
TPR1 sequences |
Amino Acid |
52 |
34 |
|
|
|
M1470
|
Crown-only 83-taxon 18S rRNA |
Legacy TreeBASE Matrix ID = M2280 |
Nucleic Acid |
83 |
1858 |
|
|
|
M32448
|
Folate metabolism-related genes in maize GTPCHI |
|
Amino Acid |
11 |
480 |
|
|
|
M36508
|
Harpellales Nucleotide Alignment |
|
Nucleic Acid |
25 |
912 |
|
|
|
M23452
|
Neomys MYCBPAP intron 11 |
|
Nucleic Acid |
14 |
472 |
|
|
|
M7031
|
Dataset 33 |
In the original uploaded data, L. zonata and O. iridescens were mislabeled. This is corrected in the TreeBASE-reconstructed datasets |
Amino Acid |
39 |
47953 |
|
|
|
M9915
|
McDonald et al Ammonium transporter alignment |
Ammonium transporter/ammonia permease genes |
Nucleic Acid |
513 |
3018 |
|
|
|
M19793
|
Mammal Ivd-intron-8 |
|
Nucleic Acid |
15 |
411 |
|
|
|
M3216
|
Opisthokont |
Legacy TreeBASE Matrix ID = M3879 |
Nucleic Acid |
45 |
1649 |
|
|
|
M6644
|
Rattus Alignment |
10 locus concatenation of Sahulian Rattus |
Nucleic Acid |
70 |
10457 |
|
|
|
M18382
|
AQP4.nexus |
|
Nucleic Acid |
27 |
969 |
|
|
|
M8175
|
Echis snake venom metalloproteinase amino acid alignment |
|
Amino Acid |
194 |
667 |
|
|
|
M34964
|
Murine Rodents |
|
Nucleic Acid |
66 |
12177 |
|
|
|
M5507
|
part 08 |
|
Nucleic Acid |
233 |
33849 |
|
|
|
M18371
|
ACE.nexus |
|
Nucleic Acid |
28 |
3099 |
|
|
|
M30374
|
Plethodontidae 38taxa_50NPCLs |
38taxa_50NPCLs |
Nucleic Acid |
38 |
48582 |
|
|
|
M17663
|
Alignment for Figure 1 |
Alignment of Adhesion domains for mammalian Adam sperm genes |
Nucleic Acid |
175 |
348 |
|
|
|
M8588
|
File 3 |
67 genes alignment |
Nucleic Acid |
16 |
29928 |
|
|
|
M25505
|
Histone chaperone SPT16 matrix |
|
Nucleic Acid |
11 |
1407 |
|
|
|
M1456
|
Combined data |
Legacy TreeBASE Matrix ID = M2266 |
Nucleic Acid |
51 |
5638 |
|
|
|
M21789
|
Indoleamine 2,3-Dioxygenase Alignment |
|
Amino Acid |
87 |
372 |
|
|
|
M47834
|
Hominid Primates 2 samples group1 filtered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M7129
|
37Taxa_6482_recode |
based on the amino acid sequences of 78 ribosomal proteins of 37 taxa (after exclusion of taxa with a significantly deviating amino acid composition) recoded using the six Dayhoff-groups |
Unspecified |
37 |
6482 |
|
|
|
M15943
|
Insulin receptor-like ectodomain genes and splice variants are found in both arthropods and human brain cDNA |
Sequence alignment |
Amino Acid |
46 |
133 |
|
|
|
M1901
|
Tetrapod RAG1 |
Legacy TreeBASE Matrix ID = M3254 |
Nucleic Acid |
88 |
2613 |
|
|
|
M44790
|
Entorrhizomycota 18S cat8 removed |
|
Nucleic Acid |
49 |
1267 |
|
|
|
M10274
|
ADRA2B BRCA1 VWF Codon Positions 1+2+3 |
All codon positions of the three genes |
Nucleic Acid |
50 |
5130 |
|
|
|
M2131
|
18S |
Legacy TreeBASE Matrix ID = M501 |
Nucleic Acid |
29 |
2520 |
|
|
|
M18374
|
AQP1.nexus |
|
Nucleic Acid |
26 |
636 |
|
|
|
M43512
|
Dicer clustalw_coredomains-gb |
|
Amino Acid |
1229 |
234 |
|
|
|
M1367
|
Caudata ND1-ND2-COI mtDNA |
Legacy TreeBASE Matrix ID = M2154 |
Nucleic Acid |
38 |
2115 |
|
|
|
M31059
|
Mammal 4DTv sites from 2583 single copy gene family |
4DTv sites from 2583 single copy gene family |
Nucleic Acid |
8 |
349724 |
|
|
|
M37012
|
Metazoan Choline Transporter-like Proteins |
CTLs protein sequences |
Amino Acid |
11 |
912 |
|
|
|
M22676
|
NASP TPRs 1-4 |
NASP TPRs1-4 sequences |
Amino Acid |
52 |
136 |
|
|
|
M31811
|
Primate MECP2 intron 3 |
MECP2 intron 3 |
Nucleic Acid |
44 |
1119 |
|
|
|
M21928
|
Eukaryote SSU DNA |
Nucleotide (SSU) from phylogenetic pipeline analysis |
Nucleic Acid |
247 |
1355 |
|
|
|
M11740
|
Mitochondrial Calcium Uniporter |
Based on 16 conserved proteins (MUSCLE aligned then concatenated) |
Amino Acid |
138 |
4427 |
|
|
|
M22748
|
NASP Full protein Sequences |
NASP Full protein Sequences |
Amino Acid |
52 |
968 |
|
|
|
M12386
|
Parrie et al tbx5 alignment |
Tbx5 aa alignment |
Amino Acid |
19 |
311 |
|
|
|
M21803
|
C1 proteases family |
|
Amino Acid |
68 |
455 |
|
|
|
M587
|
ATPaseReducedAminoAcid |
Legacy TreeBASE Matrix ID = M1487 |
Amino Acid |
52 |
981 |
|
|
|
M45622
|
Character Matrix figure 4 tree |
Phylogenetic relationships between GUK proteins |
Amino Acid |
47 |
271 |
|
|
|
M14582
|
372 taxa gene supermatrix |
|
Nucleic Acid |
372 |
61199 |
|
|
|
M21787
|
NAD+ Synthase Alignment |
|
Amino Acid |
142 |
664 |
|
|
|
M10931
|
Nine primate species |
Phylogeny of nine primate species based on a Bayesian analysis of concatenated data from 2030 UCE-anchored loci |
Nucleic Acid |
10 |
876159 |
|
|
|
M1976
|
Fig. 2 |
Legacy TreeBASE Matrix ID = M332 |
Nucleic Acid |
4 |
1486 |
|
|
|
M127
|
COII, cytb |
Legacy TreeBASE Matrix ID = M1510 |
Nucleic Acid |
36 |
1812 |
|
|
|
M18379
|
REN.nexus |
|
Nucleic Acid |
25 |
1221 |
|
|
|
M19792
|
Mammal Dhcr24-intron-7 |
|
Nucleic Acid |
15 |
254 |
|
|
|
M20844
|
Fig. 1M Full data |
|
Amino Acid |
67 |
14350 |
|
|
|
M1915
|
Concatenation of Nuclear Genes Segments for 57 Taxa |
Legacy TreeBASE Matrix ID = M3274 |
Nucleic Acid |
57 |
14326 |
|
|
|
M5503
|
part 04 |
|
Nucleic Acid |
233 |
31321 |
|
|
|
M16274
|
alignment allin |
|
Amino Acid |
177 |
107 |
|
|
|
M5500
|
part 01 |
|
Nucleic Acid |
233 |
36929 |
|
|
|
M36818
|
Tursiops truncatus 4B al Cgamma2 |
|
Nucleic Acid |
11 |
662 |
|
|
|
M4366
|
6,048x35 |
Legacy TreeBASE Matrix ID = M4558 |
Amino Acid |
35 |
6048 |
|
|
|
M3925
|
alpha A-crystallin |
Legacy TreeBASE Matrix ID = M637 |
Nucleic Acid |
39 |
145 |
|
|
|
M22925
|
Dact genes in chordates |
|
Nucleic Acid |
54 |
320 |
|
|
|
M21785
|
Nicotinate-Nucleotide Pyrophosphorylase Alignment |
|
Amino Acid |
139 |
352 |
|
|
|
M21927
|
Eukaryote Proteins |
Protein genes, concatenated, from phylogenetic pipeline analysis |
Amino Acid |
247 |
14295 |
|
|
|
M43465
|
Dicer muscle |
|
Amino Acid |
1255 |
11540 |
|
|
|
M36980
|
Marsilea vestita Kinesin2 Character Matrix |
|
Amino Acid |
40 |
399 |
|
|
|
M8081
|
IRBP3 |
|
Nucleic Acid |
17 |
1615 |
|
|
|
M25502
|
Histone chaperone NAP matrix |
|
Nucleic Acid |
51 |
886 |
|
|
|
M3169
|
Mitochondrial Dataset |
Legacy TreeBASE Matrix ID = M3831 |
Nucleic Acid |
133 |
2842 |
|
|
|
M18373
|
ANP.nexus |
|
Nucleic Acid |
28 |
459 |
|
|
|
M44794
|
Equine CEACAM TM domains |
|
Nucleic Acid |
11 |
180 |
|
|
|
M21615
|
L Blocks |
unmasked proteins of the large ribosomal subunit |
Amino Acid |
25 |
25373 |
|
|
|
M16931
|
Hedtke et al. frogs |
|
Nucleic Acid |
13 |
496814 |
|
|
|
M16281
|
gamma alignment BI |
|
Amino Acid |
46 |
149 |
|
|
|
M4248
|
mtnuc14 B |
Legacy TreeBASE Matrix ID = M4750 |
Nucleic Acid |
14 |
10452 |
|
|
|
M20846
|
Fig. 1M" High IOScore bacterial seqs mask |
|
Amino Acid |
67 |
11598 |
|
|
|
M10953
|
IRBP cytb |
|
Nucleic Acid |
50 |
2085 |
|
|
|
M1629
|
Housekeeping genes |
Legacy TreeBASE Matrix ID = M2876 |
Nucleic Acid |
26 |
5826 |
|
|
|
M6301
|
Combined |
A combined dataset of mitochondrial genomes and eight nuclear genes |
Nucleic Acid |
26 |
9133 |
|
|
|
M45624
|
Character Matrix figure 6 tree |
Phylogenetic tree of MAGUK proteins |
Amino Acid |
57 |
393 |
|
|
|
M47841
|
Hominid Primates 3 samples unfiltered |
|
Nucleic Acid |
16 |
1000 |
|
|
|
M7121
|
48Taxa_11544AA |
based on 11,544 amino acid positions derived from 78 ribosomal proteins of 48 taxa |
Amino Acid |
48 |
11544 |
|
|
|
M45949
|
Murinae RAxML Alignment |
Concatenated Matrix of CYTB, GHR, IRBP, BRCA1, RAG1, ACP5, and FGB7 used in RAxML reconstruction (converted to .nex) |
Nucleic Acid |
204 |
10449 |
|
|
|
M18378
|
ATP.nexus |
|
Nucleic Acid |
27 |
2790 |
|
|
|
M3209
|
18S rDNA |
Legacy TreeBASE Matrix ID = M3871 |
Nucleic Acid |
132 |
3086 |
|
|
|
M1787
|
Fig. 1 |
Legacy TreeBASE Matrix ID = M312 |
Nucleic Acid |
12 |
898 |
|
|
|
M36817
|
Tursiops truncatus 4A al Vgamma 2 |
|
Nucleic Acid |
24 |
341 |
|
|
|
M45574
|
Character Matrix figure 2 tree |
Structure of Par3 proteins in metazoans |
Amino Acid |
15 |
271 |
|
|
|
M2471
|
ITS1-ITS2 |
Legacy TreeBASE Matrix ID = M1831 |
Nucleic Acid |
62 |
2244 |
|
|
|
M605
|
Eukaryotic hsp90 |
Legacy TreeBASE Matrix ID = M1504 |
Amino Acid |
37 |
547 |
|
|
|
M1460
|
GHR (growth hormone receptor) |
Legacy TreeBASE Matrix ID = M2270 |
Nucleic Acid |
49 |
981 |
|
|
|
M21205
|
African Galagids 27 loci Gblocks |
Gblocks alignment |
Nucleic Acid |
30 |
14372 |
|
|
|
M21791
|
Kynureninase Alignment |
|
Amino Acid |
166 |
428 |
|
|
|
M47831
|
Hominid Primates 1 samples group 2 unfiltered |
|
Nucleic Acid |
6 |
999 |
|
|
|
M10272
|
Mammal DNA |
|
Nucleic Acid |
169 |
35603 |
|
|
|
M10609
|
Comparison of dog and human CEACAMs |
|
Nucleic Acid |
13 |
330 |
|
|
|
M1461
|
RAG1 |
Legacy TreeBASE Matrix ID = M2271 |
Nucleic Acid |
44 |
3053 |
|
|
|
M46678
|
Isopentenyltransferase genes IPPT large phylogeny |
IPPT domain gene phylogeny across kingdoms |
Amino Acid |
215 |
218 |
|
|
|
M30077
|
Eukaryotic root full ALPHA-PROT dataset |
|
Amino Acid |
77 |
9641 |
|
|
|
M38271
|
Myoblast determination protein 1 |
|
Amino Acid |
16 |
394 |
|
|
|
M8586
|
File 1 |
97 genes alignment |
Nucleic Acid |
15 |
46152 |
|
|
|
M4220
|
mtnuc14 A |
Legacy TreeBASE Matrix ID = M4751 |
Nucleic Acid |
14 |
7137 |
|
|
|
M23453
|
Neomys PRPF31 intron 3 |
|
Nucleic Acid |
14 |
590 |
|
|
|
M606
|
Eukaryotic cMDH |
Legacy TreeBASE Matrix ID = M1505 |
Amino Acid |
15 |
319 |
|
|
|
M5508
|
part 09 |
|
Nucleic Acid |
233 |
35246 |
|
|
|
M43464
|
Dicer mafft |
|
Amino Acid |
1255 |
13638 |
|
|
|
M37816
|
ABCB half transporters phylogeny of eight species |
|
Nucleic Acid |
40 |
1364 |
|
|
|
M11729
|
Fish perforin |
Fish perforin alignment |
Amino Acid |
39 |
439 |
|
|
|
M603
|
Eukaryotic HBS1 |
Legacy TreeBASE Matrix ID = M1502 |
Amino Acid |
13 |
269 |
|
|
|
M44787
|
Entorrhizomycota RPB01 cat8 removed |
|
Nucleic Acid |
46 |
829 |
|
|
|
M15535
|
Hsp70 amino acid alignment |
|
Amino Acid |
97 |
489 |
|
|
|
M19794
|
Mammal Nadsyn1-intron-4 |
|
Nucleic Acid |
15 |
294 |
|
|
|
M1875
|
|
Legacy TreeBASE Matrix ID = M322 |
Nucleic Acid |
20 |
345 |
|
|
|
M43501
|
Dicer clustalw_coredomains |
|
Amino Acid |
1229 |
1093 |
|
|
|
M38593
|
Dictyosteliida - Social Amoebae |
Alignment of 30 Proteins |
Amino Acid |
11 |
16456 |
|
|
|
M37819
|
ABCE+F transporters phylogeny of eight species |
|
Nucleic Acid |
32 |
1407 |
|
|
|
M47838
|
Hominid Primates 2 samples group2 filtered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M16318
|
Cetacea Hairless (Hr) and FGF5 Genes |
|
Nucleic Acid |
23 |
4374 |
|
|
|
M31341
|
Table 1 Extant Bats |
29 loci mined from Genbank |
Nucleic Acid |
815 |
20376 |
|
|
|
M15207
|
Matrix Partition 8 |
|
Nucleic Acid |
10 |
485067 |
|
|
|
M2593
|
Fig. 1 |
Legacy TreeBASE Matrix ID = M730 |
Amino Acid |
57 |
386 |
|
|
|
M57693
|
Apes mtDNA 34 x 13998 |
|
Nucleic Acid |
34 |
13998 |
|
|
|
M10875
|
Lophotrochozoa: 7,537 nucleotide positions |
Maximum likelihood |
Nucleic Acid |
49 |
7537 |
|
|
|
M32445
|
Folate metabolism-related genes in maize GDCH |
|
Amino Acid |
20 |
177 |
|
|
|
M36815
|
Tursiops truncatus 15 al J2 |
|
Nucleic Acid |
24 |
72 |
|
|
|
M23498
|
Cerberus/Dan/Gremlin gene family alignment |
Fig E4a |
Amino Acid |
55 |
121 |
|
|
|
M19797
|
Mammal Trpv-intron-8 |
|
Nucleic Acid |
15 |
184 |
|
|
|
M43793
|
Xenopus laevis carcinoembryonic antigen-related cell adhesion molecule |
|
Amino Acid |
37 |
109 |
|
|
|
M14267
|
NIP dataset (two state encoding) |
Near Intron Pair characters (binary characters with states 1/2) |
Morphological |
48 |
73593 |
|
|
|
M10443
|
Tarsiidae Based on 12S mtDNA Alignment 1 |
|
Nucleic Acid |
30 |
726 |
|
|
|
M2022
|
Fig. C1 |
Legacy TreeBASE Matrix ID = M337 |
Amino Acid |
42 |
55 |
|
|
|
M10273
|
Mammal AA |
|
Amino Acid |
169 |
11010 |
|
|
|
M2448
|
Transthyretin (intron 1) |
Legacy TreeBASE Matrix ID = M1808 |
Nucleic Acid |
21 |
901 |
|
|
|
M20784
|
Vertebrate ADH alignment |
ADH protein sequences |
Amino Acid |
82 |
389 |
|
|
|
M18380
|
UTA.nexus |
|
Nucleic Acid |
28 |
2583 |
|
|
|
M42305
|
Protein alignment for selected Core Homology Group proteins |
|
Amino Acid |
10 |
26019 |
|
|
|
M23446
|
Neomys CST6 intron 1 |
|
Nucleic Acid |
14 |
454 |
|
|
|
M25500
|
Histone chaperone CAF1C matrix |
|
Nucleic Acid |
29 |
621 |
|
|
|
M604
|
Eubacterial hsp-70 |
Legacy TreeBASE Matrix ID = M1503 |
Amino Acid |
23 |
479 |
|
|
|
M10874
|
Lophotrochozoa: 2,729 amino acid positions |
Bayesian inference |
Amino Acid |
49 |
2729 |
|
|
|
M43510
|
Dicer mafft_coredomains-gb |
|
Amino Acid |
1229 |
330 |
|
|
|
M8089
|
UTY18 |
|
Nucleic Acid |
17 |
881 |
|
|
|
M19796
|
Mammal Smo-intron-9 |
|
Nucleic Acid |
15 |
310 |
|
|
|
M1082
|
Tunicates 18S rDNA |
Legacy TreeBASE Matrix ID = M2591 |
Nucleic Acid |
47 |
1893 |
|
|
|
M336
|
complete uninode matrix |
Legacy TreeBASE Matrix ID = M1172 |
Amino Acid |
73 |
11181 |
|
|
|
M15011
|
Amphibians supermatrix |
Concatenated regions: 12S, 16S, COI, cytb, ND1, ND2, ND4, RAG1, Rho, tRNA-Leu, tRNA-Val |
Nucleic Acid |
105 |
10109 |
|
|
|
M37817
|
ABCC transporters phylogeny of eight species |
|
Nucleic Acid |
137 |
5143 |
|
|
|
M31752
|
Myxozoans 200 Protein coding genes |
|
Amino Acid |
77 |
51940 |
|
|
|
M2017
|
Fig. A1 |
Legacy TreeBASE Matrix ID = M336 |
Nucleic Acid |
27 |
1949 |
|
|
|
M18859
|
Lophophorata, 58 Taxa 155 Proteins |
58 Taxa 155 Proteins |
Amino Acid |
58 |
29896 |
|
|
|
M23444
|
Neomys ASB6 intron 2 |
|
Nucleic Acid |
14 |
1026 |
|
|
|
M23571
|
Multiple sequence alignment of APT-binding superfamily |
|
Amino Acid |
46 |
1202 |
|
|
|
M13181
|
A2AB CB1 GHR IRBP RAG2 vWF |
|
Nucleic Acid |
52 |
6768 |
|
|
|
M23449
|
Neomys HIF1AN intron 5 |
|
Nucleic Acid |
14 |
412 |
|
|
|
M40965
|
Holothuroidea Complete Dataset |
|
Nucleic Acid |
84 |
5171 |
|
|
|
M586
|
ATPaseNucleotideReduced2 |
Legacy TreeBASE Matrix ID = M1486 |
Nucleic Acid |
52 |
3009 |
|
|
|
M16621
|
G-alpha |
G protein alpha subunits |
Amino Acid |
38 |
488 |
|
|
|
M47832
|
Hominid Primates 1 sample group3 unfiltered |
|
Nucleic Acid |
6 |
1000 |
|
|
|
M42645
|
Phytophthora infestans and Pythium ultimum |
|
Amino Acid |
19 |
231 |
|
|
|
M8382
|
Mitochondrial 12s 16s anura matrice |
DNA 2 genes |
Nucleic Acid |
22 |
740 |
|
|
|
M2352
|
tubulin |
Legacy TreeBASE Matrix ID = M926 |
Nucleic Acid |
40 |
806 |
|
|
|
M4364
|
bamboozled barcode only |
Legacy TreeBASE Matrix ID = M4381 |
Nucleic Acid |
49 |
1988 |
|
|
|
M25508
|
Histone chaperone HIRA matrix |
|
Nucleic Acid |
14 |
1475 |
|
|
|
M19790
|
Mammal Agxt-intron-10 |
|
Nucleic Acid |
15 |
273 |
|
|
|
M1128
|
Fig3 |
Legacy TreeBASE Matrix ID = M2636 |
Amino Acid |
20 |
1275 |
|
|
|
M22913
|
Brachycephaloidea Tree-alignment matrix in Winclada Format |
Tree-alignment inferred under the parsimony criterion in POY with equal weights for all classes of transformations using the direct optimization and iterative pass optimization algorithms |
Nucleic Acid |
456 |
23241 |
|
|
|
M7124
|
30Taxa_11544AA |
based on 11,544 amino acid positions derived from 78 ribosomal proteins of 30 taxa |
Amino Acid |
30 |
11544 |
|
|
|
M45110
|
Aquaporins in mudskippers BI |
BI protein matrix of vertebrate aquaporins |
Amino Acid |
313 |
394 |
|
|
|
M32435
|
Folate metabolism-related genes in maize 5-FCL |
|
Amino Acid |
18 |
374 |
|
|
|
M35273
|
Metazoan Caspase |
|
Amino Acid |
103 |
238 |
|
|
|
M21477
|
Euungulata cytb |
|
Nucleic Acid |
306 |
1140 |
|
|
|
M1045
|
Fibrillar Collagen Major Triple Helical Domain |
Legacy TreeBASE Matrix ID = M2558 |
Amino Acid |
27 |
1060 |
|
|
|
M16282
|
gamma alignment ML |
|
Amino Acid |
46 |
149 |
|
|
|
M32450
|
Folate metabolism-related genes in maize MS |
|
Amino Acid |
17 |
1267 |
|
|
|
M12824
|
Turtles 1145 loci |
|
|
10 |
465241 |
|
|
|
M21617
|
Crassostrea gigas nuclear receptor aa sequences matrix |
alligned nuclear receptor amino acid sequences of DBD plus LBD |
Amino Acid |
131 |
221 |
|
|
|
M8462
|
10 16 Sub 90 DNA |
Nucleotide section of concatenaed dataset |
Nucleic Acid |
89 |
1205 |
|
|
|
M37269
|
Olfaction Transcriptome alignment of Fig. 3 |
|
Amino Acid |
57 |
377 |
|
|
|
M4694
|
5,216x35 |
Legacy TreeBASE Matrix ID = M4559 |
Amino Acid |
35 |
5216 |
|
|
|
M22743
|
NASP TPR2 |
TPR2 sequence curated with TrimAl |
Amino Acid |
52 |
119 |
|
|
|
M9471
|
5 genes dataset trimmed |
trimmed alignment of 4 protein codeing genes and SSU rRNA gene |
Combination |
70 |
3016 |
|
|
|
M38542
|
Paratya australiensis GPx |
|
Nucleic Acid |
32 |
191 |
|
|
|
M47829
|
Hominid Primates 1 sample group1 unfiltered |
|
Nucleic Acid |
6 |
1000 |
|
|
|
M38435
|
Placental Mammal Diversification atol122 |
|
Nucleic Acid |
122 |
35603 |
|
|
|
M25503
|
Histone chaperone NASP matrix |
|
Nucleic Acid |
9 |
889 |
|
|
|
M43466
|
Dicer clustalw |
|
Amino Acid |
1255 |
8041 |
|
|
|
M8454
|
SSU-Mask Deleted |
492 taxon SSU alignment with ambiguous bases removed |
Nucleic Acid |
492 |
1267 |
|
|
|
M3025
|
HBB spacer 3 |
Legacy TreeBASE Matrix ID = M3626 |
Nucleic Acid |
5 |
15000 |
|
|
|
M16617
|
opsins |
opsins |
Amino Acid |
60 |
536 |
|
|
|
M1118
|
GSKaa |
Legacy TreeBASE Matrix ID = M2624 |
Amino Acid |
139 |
348 |
|
|
|
M6404
|
Echis serine protease DNA alignment |
|
Nucleic Acid |
32 |
780 |
|
|
|
M45621
|
Character Matrix figure 5 tree |
Domain composition of Crumbs proteins |
Amino Acid |
47 |
71 |
|
|
|
M21940
|
First exon of Catsper1 gene (murid species) |
Alignment of the first exon of Catsper1 gene (murid species) |
Nucleic Acid |
16 |
1080 |
|
|
|
M22914
|
Brachycephaloidea Mafft-alignment |
Maximum likelihood in Garli and parsimony tree in TNT |
Nucleic Acid |
456 |
17233 |
|
|
|
M2240
|
vWF 18 taxa |
Legacy TreeBASE Matrix ID = M621 |
Nucleic Acid |
18 |
1251 |
|
|
|
M9336
|
Eutherian c-Myc sequences |
|
Nucleic Acid |
20 |
1389 |
|
|
|
M47835
|
Hominid Primates 2 samples group1 unfiltered |
|
Nucleic Acid |
11 |
1000 |
|
|
|
M7729
|
Untitled Character Matrix |
|
Amino Acid |
62 |
2973 |
|
|
|
M3170
|
Complete Dataset |
Legacy TreeBASE Matrix ID = M3832 |
Nucleic Acid |
135 |
4362 |
|
|
|
M24363
|
Cetacea Alignment Type II Keratin |
|
Nucleic Acid |
234 |
4319 |
|
|
|
M7128
|
48Taxa_6482_recode |
based on the amino acid sequences of 78 ribosomal proteins of 48 taxa recoded using the six Dayhoff-groups |
Unspecified |
48 |
6482 |
|
|
|
M23447
|
Neomys GALNT5 intron 4 |
|
Nucleic Acid |
14 |
577 |
|
|
|
M8083
|
SMCY7 |
|
Nucleic Acid |
17 |
463 |
|
|
|
M42033
|
Myotis 68x123 |
|
Amino Acid |
68 |
123 |
|
|
|
M23418
|
All Mariner Transposase |
|
Amino Acid |
74 |
460 |
|
|
|
M16929
|
Anura no missing |
|
Nucleic Acid |
13 |
8473 |
|
|
|
M8086
|
TP2 |
|
Nucleic Acid |
17 |
894 |
|
|
|
M10507
|
Cytb |
|
Nucleic Acid |
658 |
1140 |
|
|
|
M15204
|
Matrix Partition 5 |
|
Nucleic Acid |
|
750000 |
|
|
|
M43467
|
Dicer supertree |
|
Amino Acid |
1255 |
12619 |
|
|
|
M11013
|
filtered dataset |
filtered dataset (24% of sites removed) |
Amino Acid |
55 |
8741 |
|
|
|
M3155
|
5 genes |
Legacy TreeBASE Matrix ID = M3813 |
Nucleic Acid |
43 |
4364 |
|
|
|
M32444
|
Folate metabolism-related genes in maize FTHS |
|
Amino Acid |
10 |
977 |
|
|
|
M10091
|
2871 amphibians Part B |
|
Nucleic Acid |
2872 |
5810 |
|
|
|
M16924
|
Bossuyt PAUP Time |
|
Nucleic Acid |
124 |
1416 |
|
|
|
M8383
|
Combined Mitochondrial 12s 16s and Nuclear rhodopsin anura matrice |
DNA 3 genes |
Nucleic Acid |
20 |
1022 |
|
|
|
M18381
|
UTB.nexus |
|
Nucleic Acid |
31 |
735 |
|
|
|
M39729
|
CeDGAT1 and DGATs from plants, animals, fungi and microalgae |
Phylogenetic relationship between CeDGAT1 and DGATs from plants, animals, fungi and microalgae. |
Amino Acid |
45 |
1160 |
|
|
|
M4539
|
Ribosomal proteins |
Legacy TreeBASE Matrix ID = M4597 |
Amino Acid |
59 |
12428 |
|
|
|
M585
|
ATPaseNucleotideReduced1 |
Legacy TreeBASE Matrix ID = M1485 |
Nucleic Acid |
63 |
3009 |
|
|
|
M32451
|
Folate metabolism-related genes in maize MTHFR |
|
Amino Acid |
13 |
697 |
|
|
|
M61771
|
Rattus Sundaland 57x11339 |
|
Nucleic Acid |
57 |
11339 |
|
|
|
M8908
|
Aplacophorans |
|
|
51 |
2055 |
|
|
|
M23497
|
Tgf-beta gene superfamily alignment |
Fig E2 |
Amino Acid |
162 |
165 |
|
|
|
M30261
|
CDK MUSCLE alignment |
|
Amino Acid |
60 |
226 |
|
|
|
M1469
|
vWF ar adra2b |
Legacy TreeBASE Matrix ID = M2279 |
Nucleic Acid |
60 |
4566 |
|
|
|
M6414
|
Echis snake venom metalloproteinase DNA alignment |
|
Nucleic Acid |
209 |
2004 |
|
|
|
M1904
|
Appendix 2 |
Legacy TreeBASE Matrix ID = M325 |
Morphological |
9 |
94 |
|
|
|
M44182
|
Placental Mammals MC5R |
MC5R coding sequences |
Nucleic Acid |
115 |
1033 |
|
|
|
M2359
|
18S rDNA - Eumycota |
Legacy TreeBASE Matrix ID = M932 |
Nucleic Acid |
43 |
1660 |
|
|
|
M3113
|
Concatenated 65 gene matrix A |
Legacy TreeBASE Matrix ID = M3755 |
Amino Acid |
77 |
9918 |
|
|
|
M2248
|
12S |
Legacy TreeBASE Matrix ID = M629 |
Nucleic Acid |
27 |
426 |
|
|
|
M39917
|
Olfactory Marker Protein Gene Alignment |
Protein coding sequences for olfactory marker protein gene |
Nucleic Acid |
133 |
541 |
|
|
|
M43509
|
Dicer clustalw-gb |
|
Amino Acid |
1255 |
631 |
|
|
|
M23500
|
Smad gene family alignment |
Fig E5 |
Amino Acid |
76 |
115 |
|
|
|
M18750
|
SCD DNA |
|
Nucleic Acid |
73 |
720 |
|
|
|
M32443
|
Folate metabolism-related genes in maize FPGS |
|
Amino Acid |
19 |
627 |
|
|
|
M43511
|
Dicer muscle_coredomains-gb |
|
Amino Acid |
1229 |
318 |
|
|
|
M19789
|
Mammal Abcb9-intron-2 |
|
Nucleic Acid |
15 |
280 |
|
|
|
M32439
|
Folate metabolism-related genes in maize DHC |
|
Amino Acid |
23 |
408 |
|
|
|
M2449
|
mtDNA (all taxa) |
Legacy TreeBASE Matrix ID = M1809 |
Nucleic Acid |
59 |
1824 |
|
|
|
M2997
|
ann moll arth |
Legacy TreeBASE Matrix ID = M3597 |
Nucleic Acid |
131 |
5059 |
|
|
|
M20845
|
Fig. 1 M' Fast-site removal |
|
Amino Acid |
67 |
11333 |
|
|
|
M3174
|
Ribosomal Protein Alignment |
Legacy TreeBASE Matrix ID = M3836 |
Amino Acid |
39 |
11445 |
|
|
|
M3024
|
HBB spacer 4 |
Legacy TreeBASE Matrix ID = M3625 |
Nucleic Acid |
5 |
10856 |
|
|
|
M53249
|
SUMO protease domai figure 2Bs |
SUMO protease domain |
Amino Acid |
30 |
493 |
|
|
|
M5505
|
part 06 |
|
Nucleic Acid |
233 |
40861 |
|
|
|
M7137
|
48Taxa_6482_recode_0-5 |
based on the amino acid sequences of 78 ribosomal proteins of 48 taxa recoded using the six Dayhoff-groups |
Unspecified |
48 |
6482 |
|
|
|
M18751
|
SCD AA |
|
Amino Acid |
16 |
389 |
|
|
|
M43508
|
Dicer mafft-gb |
|
Amino Acid |
1255 |
859 |
|
|
|
M25504
|
Histone chaperone SPT6 matrix |
|
Nucleic Acid |
15 |
2026 |
|
|
|
M2353
|
SSU+LSU |
Legacy TreeBASE Matrix ID = M927 |
Nucleic Acid |
27 |
3660 |
|
|
|
M47828
|
Hominid Primates 1 sample group1 filtered |
|
Nucleic Acid |
6 |
1000 |
|
|
|
M2032
|
rDNA |
Legacy TreeBASE Matrix ID = M346 |
Nucleic Acid |
64 |
1620 |
|
|
|
M44213
|
Cytochrome P450 genes Fig5 |
|
Amino Acid |
33 |
785 |
|
|
|
M5506
|
part 07 |
|
Nucleic Acid |
233 |
33618 |
|
|
|
M30373
|
Plethodontidae 37taxa_50NPCLs |
37taxa_50NPCLs |
Nucleic Acid |
37 |
48582 |
|
|
|
M10951
|
cytb |
|
Nucleic Acid |
35 |
1140 |
|
|
|
M8082
|
mtDNA |
|
Nucleic Acid |
17 |
16860 |
|
|
|
M20516
|
Leot PLAC8 ALNM |
|
Amino Acid |
16 |
227 |
|
|
|
M8091
|
Xq13.3 |
|
Nucleic Acid |
17 |
6634 |
|
|
|
M15205
|
Matrix Partition 6 |
|
Nucleic Acid |
10 |
750000 |
|
|
|
M3114
|
Concatenated 85 gene matrix B |
Legacy TreeBASE Matrix ID = M3756 |
Amino Acid |
77 |
11234 |
|
|
|
M45945
|
Murinae BEAST Alignment |
Concatenated Matrix of CYTB, GHR, IRBP, BRCA1, RAG1, ACP5, and FGB7 with Partition block from PartitionFinder v1.1.1 |
Nucleic Acid |
204 |
10449 |
|
|
|
M8569
|
GST gene tree |
Human and Insect GSTs |
Amino Acid |
168 |
383 |
|
|
|
M20996
|
Metazoan Cyclin |
|
Amino Acid |
88 |
235 |
|
|
|
M7134
|
48Taxa_7671AA |
based on 7,671 amino acid positions derived from the 52 ribosomal proteins with the least heterogeneity |
Unspecified |
48 |
7671 |
|
|
|
M2575
|
SINE presence-absence |
Legacy TreeBASE Matrix ID = M2820 |
Unspecified |
23 |
31 |
|
|
|
M15206
|
Matrix Partition 7 |
|
Nucleic Acid |
10 |
750000 |
|
|
|
M602
|
Eukaryotic HMG-CoA |
Legacy TreeBASE Matrix ID = M1501 |
Amino Acid |
17 |
251 |
|
|
|
M157
|
IRBP (exon 1) |
Legacy TreeBASE Matrix ID = M1810 |
Nucleic Acid |
39 |
945 |
|
|
|
M38414
|
Raith et al combined |
|
Nucleic Acid |
233 |
1163 |
|
|
|
M622
|
c-myc/RAG1 nuDNA |
Legacy TreeBASE Matrix ID = M1521 |
Nucleic Acid |
46 |
4483 |
|
|
|
M7133
|
32Taxa_10469AA |
based on 10,469 amino acid positions derived from 71 ribosomal proteins of 32 taxa (after exclusion of taxa with a significantly deviating amino acid composition) for which the CAT model is not significantly violated |
Unspecified |
32 |
10469 |
|
|
|
M3568
|
PDHA1 |
Legacy TreeBASE Matrix ID = M734 |
Nucleic Acid |
37 |
4220 |
|
|
|
M37818
|
ABCD transporters phylogeny of eight species |
|
Nucleic Acid |
20 |
1206 |
|
|
|
M7132
|
48Taxa_10469AA |
based on 10,469 amino acid positions derived from 71 ribosomal proteins of 48 taxa for which the CAT model is not significantly violated |
Unspecified |
48 |
10469 |
|
|
|
M6402
|
Echis serine protease amino acid alignment |
|
Amino Acid |
27 |
260 |
|
|
|
M21476
|
Lagomorpha cytb |
|
Nucleic Acid |
74 |
1140 |
|
|
|
M14828
|
Haptophyta |
|
Amino Acid |
37 |
6048 |
|
|
|
M2242
|
12S-16S 43 taxa |
Legacy TreeBASE Matrix ID = M623 |
Nucleic Acid |
43 |
2086 |
|
|
|
M32447
|
Folate metabolism-related genes in maize GDCT |
|
Amino Acid |
9 |
434 |
|
|
|
M202
|
LSU rRNA |
Legacy TreeBASE Matrix ID = M1025 |
Nucleic Acid |
35 |
848 |
|
|
|
M5436
|
Concatenated Dataset |
12S = 1-750; Cox1 = 751-1500; Cox3 = 1501-2250; Cyt-b = 2251-3000; NADH-1 = 3001-3750; NADH-2 = 3751-4500; NADH-4 = 4501-5250; NADH-5 = 5251-6000; 18S = 6001-6750; 28S = 6751-7500; bdnf = 7501-8250; rag1 = 8251-9000; |
Nucleic Acid |
28 |
9000 |
|
|
|
M23451
|
Neomys MCM3 intron 2 |
|
Nucleic Acid |
14 |
419 |
|
|
|
M21614
|
MRPs Gblocks concatenated |
concatenated alignment of MRPs trimmed with Gblocks |
Amino Acid |
25 |
8456 |
|
|
|
M7130
|
48Taxa_8851_bin12_recode |
based on the amino acid sequences of 78 ribosomal proteins recoded using 12 minmax chi-squared bins |
Unspecified |
48 |
8851 |
|
|
|
M1459
|
mtDNA (COI, COII, ATPase 8) |
Legacy TreeBASE Matrix ID = M2269 |
Nucleic Acid |
45 |
1158 |
|
|
|
M5502
|
part 03 |
|
Nucleic Acid |
233 |
30623 |
|
|
|
M36507
|
Harpellales Amino Acid Alignment |
|
Amino Acid |
25 |
304 |
|
|
|
M1973
|
Myosin II |
Legacy TreeBASE Matrix ID = M3327 |
Nucleic Acid |
22 |
436 |
|
|
|
M16319
|
Cetacea Hairless (Hr) |
|
Nucleic Acid |
23 |
3564 |
|
|
|
M15200
|
Matrix Partition 2 |
|
Nucleic Acid |
|
750000 |
|
|
|
M16272
|
alignment allin |
Copper-binding sites |
Amino Acid |
179 |
107 |
|
|
|
M4292
|
ThyA |
Legacy TreeBASE Matrix ID = M4805 |
Amino Acid |
368 |
1355 |
|
|
|
M23499
|
LhX/Lim transcription factor gene family alignment |
Fig E4b |
Amino Acid |
80 |
201 |
|
|
|
M19795
|
Mammal Rras-intron-4 |
|
Nucleic Acid |
15 |
421 |
|
|
|
M1458
|
AP5 |
Legacy TreeBASE Matrix ID = M2268 |
Nucleic Acid |
37 |
446 |
|
|
|
M3208
|
18S 28S Combined |
Legacy TreeBASE Matrix ID = M3870 |
Nucleic Acid |
126 |
4842 |
|
|
|
M23450
|
Neomys JMJD intron 2 |
|
Nucleic Acid |
14 |
1038 |
|
|
|
M599
|
Eubacterial Chaperonin 60 |
Legacy TreeBASE Matrix ID = M1499 |
Amino Acid |
22 |
513 |
|
|
|
M36981
|
Marsilea vestita Kinesin9 Character Matrix |
|
Amino Acid |
24 |
501 |
|
|
|
M30376
|
Plethodontidae 38taxa_50NPCLs_Ensatina_eschscholtzii_excluded |
38taxa_50NPCLs_Ensatina_eschscholtzii_excluded |
Nucleic Acid |
37 |
48582 |
|
|
|
M2243
|
A2AB 18 taxa |
Legacy TreeBASE Matrix ID = M624 |
Nucleic Acid |
18 |
1134 |
|
|
|
M44205
|
Rana MHCII exon2 |
|
Nucleic Acid |
51 |
289 |
|
|
|
M16618
|
TRP |
transient receptor potential channels |
Amino Acid |
32 |
601 |
|
|
|
M45250
|
Kryptolebias Fig. 5 CYP 2k |
|
Amino Acid |
33 |
527 |
|
|
|
M10090
|
2871 amphibians Part A |
|
Nucleic Acid |
2872 |
6902 |
|
|
|
M4780
|
Metazoan wnts |
Legacy TreeBASE Matrix ID = M5070 |
Amino Acid |
90 |
584 |
|
|
|
M32446
|
Folate metabolism-related genes in maize GDCP |
|
Amino Acid |
11 |
1291 |
|
|
|
M37820
|
ABCG transporters phylogeny of eight species |
|
Nucleic Acid |
124 |
2212 |
|
|
|
M8080
|
DBY5 |
|
Nucleic Acid |
17 |
1048 |
|
|
|
M19798
|
Mammal Wls-intron-7 |
|
Nucleic Acid |
15 |
351 |
|
|
|
M3156
|
18S-28S |
Legacy TreeBASE Matrix ID = M3814 |
Nucleic Acid |
72 |
1818 |
|
|
|
M8587
|
File 2 |
82 genes alignment |
Nucleic Acid |
17 |
36441 |
|
|
|
M38413
|
Raith et al. 16S |
|
Nucleic Acid |
903 |
1670 |
|
|
|