Table 1.

Command-line options available in 2matrix.

Option flaga	Description	Required for operation
-d	Produce output without coded indels (the default is to code indels).	No
-i file-name	Specify input files (aligned FASTA, csv, or xread [cf. Hennig86, NONA, WinClada]). If several files are to be merged, file names should be input with multiple “-i” flags.	Yes
-n root-name	Specify the root name for output files.	Yes
-o format	Specify the output file format: “-o x” for xread; “-o n” for NEXUS; “-o p” for extended PHYLIP. If NEXUS format is selected, files compatible with both Garli (“root-name.garli.nex”) and MrBayes (“root-name.mrbayes.nex”) will be created. Additionally, a Garli configuration file will be automatically generated (“root-name.conf”). If PHYLIP format is selected, a RAxML partition file will automatically be created (“root-name.part”).	Yes
-s stem-name	Specify the stem name to be used for sequence and indel characters in xread and NEXUS files. If characters are to be named, there must be an “-s” flag for each FASTA file (the “-s” and “-i” flags should be in the same order).	No

^aItalicized text following option flags should be specified by the user.