TreeBASE Search-Analyses for study 12173

@ARTICLE{TreeBASE2Ref20255, author = {P. Roxanne Steele and Kate L Hertweck and Dustin Mayfield and Michael R. McKain and Jim Leebens-Mack and J. Chris Pires}, title = {Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae}, year = {2012}, keywords = {angiosperms; Aphyllanthes; chloroplast; mitochondria; next generation sequencing; nuclear ribosomal DNA; phylogenetics; plastid}, doi = {}, url = {http://}, pmid = {}, journal = {American Journal of Botany}, volume = {}, number = {}, pages = {}, abstract = {Premise of the study: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective datasets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80-120 bp reads. Methods: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in non-model taxa. Key results: Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confidence. Conclusions: The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.} }

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Analyses for Study 12173

Citation title: "Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae".

Study name: "Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae".

This study is part of submission 12173 (Status: Published).

Analyses

Analysis 1

Analysis details

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3 Input object(s)

Analysis step

CombinedMP --

Step details

Name

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Name
Algorithm
Commands
>Heuristic search settings: > Optimality criterion = parsimony > Character-status summary: > Of 79286 total characters: > All characters are of type 'unord' > All characters have equal weight > 56197 characters are constant > 10261 variable characters are parsimony-uninformative > Number of parsimony-informative characters = 12828 > Gaps are treated as "missing" > Starting tree(s) obtained via stepwise addition > Addition sequence: random > Number of replicates = 100 > Starting seed = 1972318490 > Number of trees held at each step during stepwise addition = 10 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > No more than 100 trees of score (length) greater than or equal to 1 will be > saved in each replicate > Initial 'MaxTrees' setting = 5000 (will be auto-increased by 100) > Branches collapsed (creating polytomies) if maximum branch length is zero > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1776954 > Score of best tree(s) found = 49515 > Number of trees retained = 1 > Time used = 00:03:33 (CPU time = 00:03:33.0)

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

cpDNAMP --

Step details

Name

Software used

Name
Algorithm
Commands
>Data file = /Users/steelepr/01-Aspar-MP500.dat >Heuristic search settings: > Optimality criterion = parsimony > Character-status summary: > Of 73585 total characters: > All characters are of type 'unord' > All characters have equal weight > 51725 characters are constant > 9516 variable characters are parsimony-uninformative > Number of parsimony-informative characters = 12344 > Gaps are treated as "missing" > Starting tree(s) obtained via stepwise addition > Addition sequence: random > Number of replicates = 100 > Starting seed = 27220680 > Number of trees held at each step during stepwise addition = 10 > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > No more than 100 trees of score (length) greater than or equal to 1 will be > saved in each replicate > Initial 'MaxTrees' setting = 5000 (will be auto-increased by 100) > Branches collapsed (creating polytomies) if maximum branch length is zero > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2167995 > Score of best tree(s) found = 47266 > Number of trees retained = 1 > Time used = 00:03:30 (CPU time = 00:03:30.3)

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

3 Input object(s)

Analysis step

CombinedML --

Output data

1 Output object(s)

Input data

1 Input object(s)

Analysis step

cpDNAML --

Output data

1 Output object(s)

Input data

1 Input object(s)

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mtDNAML --

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1 Output object(s)

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1 Input object(s)

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nrDNAML --

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