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- list.seqs - reads one of the following file types: fasta, name, group or alignreport file and writes out the names of the sequences found within it.
- get.seqs - reads an .accnos file and one of the following file types: fasta, name, group or alignreport file. It outputs a file containing only the sequences in the .accnos file.
- remove.seqs - reads an .accnos file and one of the following file types: fasta, name, group or alignreport file. It outputs a file containing the sequences NOT in the .accnos file.
- system - Allow the user to enter system commands from within mothur.
- added sorted option to get.rabund.
- improved clustering algorithm to increase speed with marginal memory cost [thanks to Gerhard Thallinger]
- mothur can now read trees that include internal node labels (e.g. bootstrap values), but can only take in bifurcating trees.
- read.otu with list and groups now outputs .rabund files instead of .list files.
- fixed windows unable to open file error with filter.seqs.
- fixed bug with help command.
- fixed bug with batchfile input.
- fixed bug that resulted in an infinite loop if user forgot ; in ScriptBatchEngine.
- fixed bug in venn with 4 groups that gave inflated values.
- fixed bug with aligner that occurred when template sequence names contained spaces.
- fixed bug in simpson calculator that occurred whenever the number of sequences exceeded the maximum size of an int