Option	Description
-u	Union mode – Includes individuals in output file from input files that are not necessarily represented by every input file. Missing regions are padded with ‘?’ characters. Note: this feature is enabled by default and is mutually exclusive to intersection mode described below.
-i	Intersection mode – Excludes any individual that is not represented by every input locus.
-rc [x -y[,…,x-y]]	Remove column – Takes a range of columns, hyphen delimited, or a list of ranges, comma delimited, and removes them from the final output file. Note: There should be no spaces between the hyphens or commas.
-rr [x-y[,…,x-y]]	Remove row – Takes a range of rows, hyphen delimited, or a list of ranges, comma delimited, and removes them from the final output file. Note: There should be no spaces between the hyphens or commas.
-I	Interleave output – Sets the sequence formatting to interleaved instead of sequential, which is the default setting, for the specific output type specified by the output files extension.

 

SUPPORTED FORMATS
Combine allows the user to specify their desired output format implicitly via the file name extension for the output file. Additionally each supported file has both a sequential and an interleaved sub-format which is specified with the –I flag. The supported files extensions are listed below:

 

	Extension
NEXUS	nxs
CLUSTAL	aln
FASTA	fas
PHYLIP	phy

 

Each of these file types is also supported as an input file format. Input file types in Combine are determined internally by the actual content of the file, not its filename extension. Therefore input files do not necessarily have to follow the same filename extension conventions used to determine output file format.

Also included in this distribution is MLCombine, a java program which combines multiple single locus MIGRATE infiles generated using SNAP Map into a single multilocus MIGRATE infile.

  COMMAND LINE

      java –jar MLCombine.jar OUTFILE [MIGRATE INFILE [... MIGRATE INFILE]]