NAME¶

ancestral_reconstruction - Reconstructs ancestral sequences and maps mutations to the tree

SYNOPSIS¶

ancestral_reconstruction [-h] --aln ALN --tree TREE [--prot] [--marginal] [--infer_gtr] [--keep_overhangs]

DESCRIPTION¶

Reconstructs ancestral sequences and maps mutations to the tree. The output consists of a file ending with _ancestral.fasta with ancestral sequences and a tree ending with _mutation.nexus with mutations added as comments like _A45G_... The inferred GTR model is written to stdout

OPTIONS¶

-h, --help

show this help message and exit

--aln ALN

fasta file with input sequences

--tree TREE

newick file with tree

--prot

protein alignment

--marginal

marginal instead of joint ML reconstruction

--infer_gtr

infer substitution model

--keep_overhangs

do not fill terminal gaps

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.