SIMPLE SOLUTIONS

ANCESTRAL_RECONSTRUCTION(1) - Linux man page online | User commands

Reconstructs ancestral sequences and maps mutations to the tree.

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June 2017
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)
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