Man pages sections > man1 > ancestral_reconstruction

ancestral_reconstruction - Reconstructs ancestral sequences and maps mutations

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 _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.
June 2017 ancestral_reconstruction 0.0+20170607