Table 1 New tool wrappers developed thus far for phylogenetic analyses in Galaxy

Get data

Get GB

*

Grab Genbank data from a text list of accession numbers

Get GB sp

*

Grab all GenBank data from a text list of species

PhyLoTA with TaxID

*

Pull all genetic data from PhyLoTA using a GenBank Taxonomy ID

Generate from PhyLoTA

*

Pull phylogenies and genetic data from PhyLoTA with species list

GenBank strip

*

Extracts sequences from GenBank files by gene name

GB gene summary

*

Summarizes gene names in a GenBank flatfile

Get Sequences

*

Creates a file of selected sequences

Orthologs

EvolMap

[13]

Uses species tree and gene distances to determine orthologs and paralogs

HaMStR

[14]

Pulls orthologous genes from an input file based on HMM gene models

HMMbuild

[15, 16]

Constructs Hidden Markov Models from aligned sequences

HMMsearch

[15, 16]

Searches for similar genes using HMM models

Alignment

Phytab-MUSCLE

[17]

Implements MUSCLE multiple sequence alignment for multiple gene families in parallel

Phytab-PRANK

[18]

Implements PRANK phylogeny aware multiple sequence alignment

Mview

[19]

Converts an aligned sequences file in fasta format to html for visualization

Phytab-MAFFT

[20]

Implements MUSCLE multiple sequence alignment for multiple gene families in parallel

Alicut and Aliscore

[21]

Implements Alicut and Aliscore to prune ambiguous alignments for multiple gene families in parallel

Gblocks

[22]

Implements gblocks to prune ambiguous alignments

Phytab- Similar Sequence Remover

*

Removes percentage of similar sequences using Phytab input

Sequence Gap Remover

*

Removes gaps from columns of an aligned phylip file

Trimming Sites

[13]

Allows user to delete sites from an alignment based on percentage threshold

Phylocatenator

*

Concatenates phytab datasets based on user-specified criteria and writes phylipE format. Also produces partition file for RAxML

Fasconcat

[23]

Concatenates input sequence files using Phylip, Clustal or FASTA input

Phyloconversion

tnt2table

*

Converts TNT file format from Morphobank into phytab format

fasta2phylipE

*

Converts fasta format to phylipE format

Beautifyfasta

*

Converts fasta interleaved format to sequential

Addstring2fashead

*

Converts fasta file with sequences from same species and gene family to phytab format

Length Outliers

*

Identifies sequences shorter than average in FASTA file

Vert_tree_format

[24]

Convert between phylogenetic tree file formats

Prune Phytab using list

*

Filters Phytab dataset based on user provided list

Removes Phytab dupes

*

Finds duplicates in Phytab file

Phylogenies

RAxML

[25]

Implements maximum likelihood (ML) search for optimal phylogeny

Phytab-RAxML-Parsimony

[25]

Searches for MP phylogeny of multiple data partitions simultaneously

Phytab-RAxML

[25]

Searches for ML phylogeny of multiple data partitions simultaneously

Phytab-RAxML using starting trees

[25]

Optimizes branch lengths on a starting tree. Multiple partitions simultaneously

BEAST

[1]

Executes xml for Bayesian phylogenetic analysis

RAxML-Place Fossil

[25, 26]

Finds fossil position on a tree using morphological data and input phylogeny

NJst

[27]

Produces species tree from input of multiple gene trees

RAxML Place reads

[26]

Uses RAxML to place sequence reads onto an existing phylogeny

RAxML Parsimony

[25]

Uses RAxML to calculate a parsimony tree

Phytab clearcut

[28]

Generate Neighbor Joining phylogeny. Input can be FASTA or Phytab format

ProtTest

[29]

Selection of best-fit models of protein evolution

jModelTest

[30]

Selection of best-fit models of nucleotide evolution

tab2trees

*

Produces phylogeny graphics, one tree per page, from multiple data partitions or data sets

Phylographics

PDpairs

*

Calculates phylogenetic distances for pairs of species on a phylogeny

Phylostatistics

Phytab LB pruner

Identify genes on very long branches

Long Branch Finder

*

Identifies terminal branches on multiple gene trees which exceed a threshold

Phylomatic

[31]

Implements phylomatic program

Tree Support

[24]

Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees

Branch Attachment Frequency

[24]

Identifies lineage movement in a set of trees

Leaf Stability

[24]

Reports leaf stability indices for taxa in tree/trees

TreeAnnotator

[1]

Calculates summary statistics from posterior distribution of bayesian trees

Prune Taxa

[24]

Removing taxa from a tree or multiple trees

Thinning Trees

[24]

Sub-sample trees from a posterior distribution

SHtest

[25]

Uses RAxML to compute an SHtest to compare trees