TreeBASE Search-Analyses for study 13843

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Analyses for Study 13843

Citation title: "Testing a Hypothesis of Intergeneric Allopolyploidy in Vine Cacti (Cactaceae: Hylocereeae)".

Study name: "Testing a Hypothesis of Intergeneric Allopolyploidy in Vine Cacti (Cactaceae: Hylocereeae)".

This study is part of submission 13843 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ITSC1 RAxML Analysis --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
Sequence type set to nucleotide; Outgroup set to Stenocereus griseus and Stenocereus gummosus; Estimate proportion of invariable sites (GTRGAMMA + I) set to no; Find best tree using maximum likelihood search set to yes; Mixed partition model used (DNA,18s = 1-33 DNA,its1 = 34-250 DNA,5p8s = 251-413 DNA,its2 = 414-621); Let RAxML halt bootstrapping automatically set to yes; Print branch lengths set to yes.

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

ITSC1 Parsimony Analysis --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
log log.log; mxram1600; p filename.tnt; xi; rs0; hold 40001; rat: it5000upf5dow5; drift: iter 50; mu=rep2000ho20; ratchet; drift; tfuse; ho500000; bbreak=tbr; tsave* filename.tre; save; tsave/; nel; tsave filename_nel.tre; save /; tsave /; k0; p filename.tnt; ho10001; rat: it200upf5dow5; mu: rep20ho20rat; resamp boot rep10000 savetrees; tsave* boot10000_filename.tre; save; tsave /; quit;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

PhyC Parsimony Analysis --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
log log.log; mxram200; p filename.tnt; xi; rs0; hold 20001; rat: it5000upf5dow5; drift: iter 50; mu=rep1000ho20; ratchet; drift; tfuse; ho10000; bbreak=tbr; tsave* filename.tre; save; tsave/; nel; nel; tsave phyC_filename_nel.tre; save /; tsave /; k0; p filename.tnt; ho1001; rat: it200upf5dow5; mu: rep20ho20rat; resamp boot rep1000 savetrees; tsave* boot1000_filename.tre; save; tsave /; quit;

Output data

1 Output object(s)

Analysis 4

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Vatp1 Parsimony Analysis --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
log log.log; mxram200; p filename.tnt; xi; rs0; hold 20001; rat: it5000upf5dow5; drift: iter 50; mu=rep1000ho20; ratchet; drift; tfuse; ho10000; bbreak=tbr; tsave* filename.tre; save; tsave/; nel; nel; tsave filename_nel.tre; save /; tsave /; k0; p filename.tnt; ho1001; rat: it200upf5dow5; mu: rep20ho20rat; resamp boot rep1000 savetrees; tsave* boot1000_filename.tre; save; tsave /; quit;

Output data

1 Output object(s)

Analysis 5

Analysis details

Name

Input data

1 Input object(s)

Analysis step

CP Parsimony Analysis --

Step details

Name

Software used

Name
Version
Description
Algorithm
Commands
log log.log; mxram800; p filename.tnt; xi; rs0; hold 40001; rat: it5000upf5dow5; drift: iter 50; mu=rep2000ho20; ratchet; drift; tfuse; ho500000; bbreak=tbr; tsave* filename.tre; save; tsave/; nel; tsave filename_nel.tre; save /; tsave /; k0; p filename.tnt; ho10001; rat: it200upf5dow5; mu: rep20ho20rat; resamp boot rep10000 savetrees; tsave* boot10000_filename.tre; save; tsave /; quit;

Output data

1 Output object(s)

Analysis 6

Analysis details

Name

Input data

1 Input object(s)

Analysis step

CP RAxML Analysis --

Step details

Name

Software used

Name
Version
URL
Algorithm
Commands
Sequence type set to nucleotide; Outgroup set to Stenocereus griseus and Stenocereus gummosus; Estimate proportion of invariable sites (GTRGAMMA + I) set to no; Find best tree using maximum likelihood search set to yes; Mixed partition model used (DNA,rpl32?trnL = 1?1478 DNA,psbD?trnT = 1479?2214 DNA,trnQ?5?rps1618s = 2215?2858); Let RAxML halt bootstrapping automatically set to yes; Print branch lengths set to yes.

Output data