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- summary.seqs - outputs statistics regarding a collection of sequences [pds]
- screen.seqs - screen sequence, name, and group files based on whether sequences satisfy user-defined criteria [pds]
- reverse.seqs - outputs the reverse complement of a file of sequences [pds]
- tree.shared command now allows you to input a phylip-formatted distance file [sw]
- added "smart" distance recognition on all commands using the label parameter [sw]
- added ability to omit () on the quit command [sw]
- the deconvolute() command is now called the unique.seqs() command.
- the bin.seqs and get.oturep commands now accept a group file. If you provide a group file they will append the group info to the sequence name and bin number [sw]
- no longer support sequence files in nexus, clustal or phylip form [sw]
- dist.seqs now has the ability to output a phylip formatted distance in addition to the column format. To do so use the parameter phylip=t [sw]
- sharedmultiple.summary file is only generated from the summary.shared command when there are more than two samples [sw]
- dist.seqs can now use n processors.
- the heatmap command is now called heatmap.bin.
- fixed infinite loop if mothur is given a non-existent batchfile [sw]
- fixed get.group() command. [sw]
- optimized summary.shared command [sw]
- ability to use -1 in a distance file to represent infinity [sw]
- tree.shared command creates trees with root to tip length of 0.5 [sw]
- fixed bug where deconvolute() would double the length of the last sequence [ps]
- fixed bug with read.dist for windows users [sw]
- fixed help for filter.seqs and align.seqs
- fixed bug with deconvolute that double the length of last sequence
- mothur now recognizes TRUE, true, T and t as true.
- removed using namespace std from all files except mothur.h and defined arrays to comply with C++ standard to better support VS.
- added <ctime> and defined math functions for windows user.
- fixed memory access violation with read.dist.
- fixed a minor bug in tree.shared command.
- get.oturep can now process aligned sequences as well as unaligned sequences.
- summary.shared command now only creates a .sharedmultiple.summary if you use sharedchao or sharedsobs, and have more than 2 groups.