2xread: a simple indel coding tool
Damon P. Little1
1Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, NY, USA
This script implements the simple gap (indel) coding method of Simmons and Ochoterena (2000) in a portable command line environment. Other similar tools include GapCoder (Young and Healy 2003) and SeqState (Müller 2003).
The output is in the form of a xread file that is compatible with NONA, TNT, WinClada, MacClade, Mesquite, etc.
The inputs for 2xread are:
(1) A DNA or RNA alignment in FASTA or dread format (output by e.g. WinClada).
(2) Optionally, a user–defined string can be used to label positions in the matrix for future reference.
2xread in_file [stem_name]
Note that “stem_name” must be interpreted as a single token by your shell. The script prints to standard out, so a redirect operator (e.g. '>') should be used to capture the output in a file.
Little, D. P. 2005. 2xread: a simple indel coding tool. Program distributed by the author.