The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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RAxML-7.3.0

RAxML implements a rapid maximum likelihood-based inference of phylogenetic trees from nucleotide or amino acid multiple sequence alignments. The phylip_interleaved.phy output of the Muscle-3.8.31 App in the Discovery Environment is suitable for this analysis.

Quick Start

  • To use RAxML, upload your data in relaxed PHYLIP format (interleaved, no name length restrictions).
  • Resources: documentation

Test Data

Use the protein alignment elong_alpha.phy as test data.  It can be accessed by navigating to :

'Community Data'->iplantcollaborative>example_data->raxml-7.3.0

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Run the test analysis with default parameters
  • Setting the *Multiple Sequence Alignment* and *Sequence Type* Parameters is mandatory.
DNA-Specific Options

There is only one option for dna sequences, the 'Substitution Model'. If this option is not set, the DNACAT option will be used by default. The RAxML descriotion of the available options is shown below:

GTRCAT
GTR + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated under GTRGAMMA, depending on the tree search option

GTRCATI
GTR + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated under GTRGAMMAI, depending on the tree search option

GTRGAMMA
GTR + Optimization of substitution rates + GAMMA model of rate heterogeneity (alpha parameter will be estimated)

GTRGAMMAI
Same as GTRGAMMA, but with estimate of proportion of invariable sites

Protein-Specific Options

Components of substitution model can be selected. The amino acid substitution model has three parts, which are joined automatically into the model name used by RAxML:

ModelmatrixNameF

The substitutionmatrix can be either BLOSSUM62 or DAYHOFF. Emprirical base Frequences F is a shown as a checkbox (checked by default).  The F option is either present or absent, depending on whether the box is checked.

By default, the PROTCAT substitution model, the BLOSSUM62 substitution matrix, and empirical amino acid frequencies (F) will be used to form the model: PROTCATBLOSSUM62F

PROTCATmatrixName(F)
specified AA matrix + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated automatically under PROTGAMMAmatrixNamef, depending on the tree search option"PROTCATImatrixNameF" : specified AA matrix + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated automatically under PROTGAMMAImatrixNamef, depending on the tree search option

PROTGAMMAmatrixName(F)
specified AA matrix + Optimization of substitution rates + GAMMA model of rate heterogeneity (alpha parameter will be estimated)

PROTGAMMAImatrixName(F)
Same as PROTGAMMAmatrixName(F), but with estimate of proportion of invariable sites

Output File(s)

  • The raw RAxML output files are saved in the RAXML_out folder

Tool Source

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1 Comment

  1. The documentation link under quick start is out of date.