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

From: Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

Analysis stage Tool Ref. Notes
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
  1. *Tools developed for Osiris.