Get data
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Get GB
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*
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Grab Genbank data from a text list of accession numbers
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Get GB sp
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*
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Grab all GenBank data from a text list of species
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PhyLoTA with TaxID
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*
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Pull all genetic data from PhyLoTA using a GenBank Taxonomy ID
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Generate from PhyLoTA
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*
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Pull phylogenies and genetic data from PhyLoTA with species list
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GenBank strip
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*
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Extracts sequences from GenBank files by gene name
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GB gene summary
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*
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Summarizes gene names in a GenBank flatfile
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Get Sequences
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*
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Creates a file of selected sequences
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Orthologs
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EvolMap
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[13]
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Uses species tree and gene distances to determine orthologs and paralogs
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HaMStR
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[14]
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Pulls orthologous genes from an input file based on HMM gene models
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HMMbuild
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[15, 16]
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Constructs Hidden Markov Models from aligned sequences
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HMMsearch
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[15, 16]
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Searches for similar genes using HMM models
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Alignment
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Phytab-MUSCLE
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[17]
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Implements MUSCLE multiple sequence alignment for multiple gene families in parallel
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Phytab-PRANK
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[18]
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Implements PRANK phylogeny aware multiple sequence alignment
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Mview
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[19]
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Converts an aligned sequences file in fasta format to html for visualization
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Phytab-MAFFT
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[20]
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Implements MUSCLE multiple sequence alignment for multiple gene families in parallel
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Alicut and Aliscore
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[21]
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Implements Alicut and Aliscore to prune ambiguous alignments for multiple gene families in parallel
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Gblocks
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[22]
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Implements gblocks to prune ambiguous alignments
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Phytab- Similar Sequence Remover
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*
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Removes percentage of similar sequences using Phytab input
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Sequence Gap Remover
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*
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Removes gaps from columns of an aligned phylip file
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Trimming Sites
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[13]
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Allows user to delete sites from an alignment based on percentage threshold
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Phylocatenator
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*
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Concatenates phytab datasets based on user-specified criteria and writes phylipE format. Also produces partition file for RAxML
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Fasconcat
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[23]
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Concatenates input sequence files using Phylip, Clustal or FASTA input
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Phyloconversion
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tnt2table
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*
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Converts TNT file format from Morphobank into phytab format
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fasta2phylipE
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*
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Converts fasta format to phylipE format
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Beautifyfasta
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*
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Converts fasta interleaved format to sequential
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Addstring2fashead
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*
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Converts fasta file with sequences from same species and gene family to phytab format
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Length Outliers
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*
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Identifies sequences shorter than average in FASTA file
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Vert_tree_format
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[24]
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Convert between phylogenetic tree file formats
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Prune Phytab using list
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*
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Filters Phytab dataset based on user provided list
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Removes Phytab dupes
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*
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Finds duplicates in Phytab file
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Phylogenies
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RAxML
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[25]
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Implements maximum likelihood (ML) search for optimal phylogeny
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Phytab-RAxML-Parsimony
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[25]
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Searches for MP phylogeny of multiple data partitions simultaneously
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Phytab-RAxML
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[25]
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Searches for ML phylogeny of multiple data partitions simultaneously
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Phytab-RAxML using starting trees
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[25]
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Optimizes branch lengths on a starting tree. Multiple partitions simultaneously
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BEAST
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[1]
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Executes xml for Bayesian phylogenetic analysis
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RAxML-Place Fossil
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[25, 26]
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Finds fossil position on a tree using morphological data and input phylogeny
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NJst
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[27]
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Produces species tree from input of multiple gene trees
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RAxML Place reads
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[26]
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Uses RAxML to place sequence reads onto an existing phylogeny
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RAxML Parsimony
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[25]
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Uses RAxML to calculate a parsimony tree
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Phytab clearcut
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[28]
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Generate Neighbor Joining phylogeny. Input can be FASTA or Phytab format
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ProtTest
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[29]
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Selection of best-fit models of protein evolution
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jModelTest
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[30]
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Selection of best-fit models of nucleotide evolution
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tab2trees
|
*
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Produces phylogeny graphics, one tree per page, from multiple data partitions or data sets
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Phylographics
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PDpairs
|
*
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Calculates phylogenetic distances for pairs of species on a phylogeny
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Phylostatistics
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Phytab LB pruner
| |
Identify genes on very long branches
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Long Branch Finder
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*
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Identifies terminal branches on multiple gene trees which exceed a threshold
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Phylomatic
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[31]
|
Implements phylomatic program
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Tree Support
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[24]
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Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees
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Branch Attachment Frequency
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[24]
|
Identifies lineage movement in a set of trees
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Leaf Stability
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[24]
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Reports leaf stability indices for taxa in tree/trees
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TreeAnnotator
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[1]
|
Calculates summary statistics from posterior distribution of bayesian trees
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Prune Taxa
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[24]
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Removing taxa from a tree or multiple trees
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Thinning Trees
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[24]
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Sub-sample trees from a posterior distribution
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SHtest
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[25]
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Uses RAxML to compute an SHtest to compare trees
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