svr_tree

    svr_tree [options] < ali.fa > tree.newick

This script uses fasttree, PhyML or RAxML to build a maximum-likelihood tree from a FASTA alignment, or evaluates the likelihood of an input tree against a given alignment.

Example: svr_tree -e -phyml -i aaa.tree < aaa.ali

would evaluate the likelihood of aaa.tree using PhyML.

Introduction

usage: svr_tree [options] < ali.fa > tree.newick

       -tool fasttree (D), phyml, raxml

       -b  n_bootstraps  - number of bootstrap samples (D = 0)
       -c  num_classes   - number of substitution categories (D = 4)
       -e                - evaluate the log likelihood of a given tree
       -g  log_file      - log file with time and likelihood information
       -i  tree_file     - input tree file for likelihood evaluation 
       -l                - construct tree locally 
       -m  model         - substitution model
       -n  num_procs     - number of processors to use for bootstraps
       -p  param_str     - parameter string for tree tool
       -r                - use gamma distribution for substitution rates
       -s                - use SPR for tree topology search (more expensive than NNI)
       -t  file_name     - output tree file (can be used in combination with -e)

Command-Line options

-b bootstraps

The number of bootstrap samples.

-c nclasses

The number of categories of substitution rates.

-e

With the -e option, the likelihood of an input tree (specified by the -i option) is evaluated.

-g log_file

The log file name.

-i tree_file

The name of tree file whose log likelihood is to be evaluated.

-l

With the -l option, tree construction or likelihood evaluation is done olocally.

-m model

Sequence substitution model:

Nucleotides:

  fasttree: GTR

  PhyML: HKY85 (d), JC69, K80, F81, F84, TN93

  RAxML: GTR

Amino acids:

  fasttree: GTR

  PhyML: LG (d), WAG, JTT, MtREV, Dayhoff, DCMut

  RAxML: WAG (d), JTT, Dayhoff, DCMUT, METREV, RTREV, CPREV, VT, BLOSSUM62, MTNAM, GTR 

-n num_procs

Number of processors to use for bootstraps.

-p param_str

The raw parameter string for a tree building tool, which may be superseded by other options if there is an overlap. It can be used to set options that are not universal to all tree building programs.

For example, in the following command, the conflicting 'model' option will be resolved to be 'JTT', but the 'search' option will be set to 'BEST' which is only available to PhyML.

svr_tree -tool=phyml -p '-m WAG -s BEST' -m JTT < ali.fa > tree.newick

-r

With the -r option, the discretized gamma distribution is used for substitution rates.

-s

With the -s option, both fasttree and PhyML will try to use the SPR (Subtree Pruning and Regrafting) operation, instead of the default, less expensive, NNI operation, in the heuristic search for the best tree topology. RAxML uses SPR by default. In fasttree, the number of SPR rounds is set to 2 by default, and it can be customized with the "-p '-spr x'" option.

t tree_file

The file name of the output tree to be saved.

Input

The input set of aligned sequences is read from STDIN.

Output

If the -e option is set, the output is the log likelihood value of the input tree; otherwise, it is the tree (in newick format) built from the input alignment.