ANCESTRAL_RECONSTRUCTION(1) User Commands ANCESTRAL_RECONSTRUCTION(1)
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 _muta‐
tion.nexus with mutations added as comments like _A45G_... The inferred GTR model is writ‐
ten 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.
ancestral_reconstruction 0.0+20170607 June 2017 ANCESTRAL_RECONSTRUCTION(1)