clone_reducer

Author: Michael R. McKain

Version 1.1, October 2014

Contact: https://github.com/mrmckain

Description

Clone_reducer identifies clades in a gene tree that comprise a single accession/species with a bootstrap value greater than or equal to what the user chooses. The clade is reduced to a consensus sequence and a new alignment file is written. The consensus is based on majority rules.

Clone reducing script used in Estep et al. (2014). doi: 10.1073/pnas.1404177111

Output

Condensed Clones File:

Final alignment file with sequences reduced.

Logfile:

Log of clones that were condensed given accession identifier.

Removed Clones:

Sequences of clones that were condensed.

Usage

perl clone_reducer.pl -alignment file -tree file [options]

Options:

-alignment          Alignment file in FASTA format used to produce gene tree
-tree               Newick tree file created from alignment
-percent_length     Percent in decimal format of unaligned sequence to alignment length [Default: 0.5]
-bootstrap          Minimum bootstrap value for clade to be considered for consensus sequence [Default: 50]
-consensus          Flag to output consensus sequence of clones
-longest            Flag to output longest sequence of clones
-help               Brief help message
-man                Full documentation