Author: Michael R. McKain
Version 1.1, October 2014
Contact: https://github.com/mrmckain
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
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.
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