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We are happy to announce the release of the mothur v.1.10.0! This release contains a number of new commands and additional features, many of which were suggested by our loyal users over on the mothur forum. There are three notable additions to this release. First, users can now generate neighbor joining trees within mothur using the clearcut command, which is a wrapper for the program by the same name. Second, we have added an additional "phylogenetic" method for assessing alpha diversity by using the phylo.diversity command. Third, we offer the make.group command, which should lighten the load of our in-box - if you give mothur the names of your fasta files that contain sequences for different groups, mothur will make the group file for you. We've also added a number of features to expand the utility of mothur including adding parallelization to many commands and the ability to have inexact matches to your primers and barcodes in the trim.seqs command.
As always, we appreciate your feedback and suggestions. Hopefully, you can see that we take your comments seriously and are happy to incorporate good ideas into mothur!
- added set.logfile command - allows user to set logfile name and/or append the log to an existing file
- added phylo.diversity command - phylogenetic diversity
- added make.group command - http://www.mothur.org/forum/viewtopic.php?f=3&t=385&sid=6260346b9aab4bf74e20f667fd135cb4
- added chop.seqs command - http://www.mothur.org/forum/viewtopic.php?f=3&t=399&sid=ecc7b9a7e046fb48f5a5345713ef3fd2
- added clearcut command - wrapper for clearcut
- http://www.mothur.org/forum/viewtopic.php?f=5&t=300&p=749&sid=80af1914178877c36516229d2fe8d809#p749 - added group parameter to classify.seqs, reworked summary file so the taxids are based on the reference taxonomy.
- made taxonomy static between runs
- speed comparison between our classify.seqs with bayesian and the RDPs. Have received reports that ours is much slower.
- added name option for phylotype command
- parallelized screen.seqs - made it MPI Enabled
- parallelized trim.seqs
- added tdiffs, bdiffs and pdiffs parameters to trim.seqs command
- made get.oturep command be made more memory efficient by breaking processing into 2 parts so distance and list files are not in memory at the same time as fasta, name and group files.
- added hard parameter to cluster, hcluster and read.dist for a hard cutoff (hard=T), where the cutoff is 0.03, not 0.0349, etc.
- remove.seqs can remove sequences from multiple files at once.
- mothur now recognizes ~, so you can enter filenames like ~/desktop/myFile.fasta, or set.dir(output=~)
- added 3 constructors to sequence class that just fill unaligned field to save space when we don't need an aligned sequence.
- made freq a percentage of number of sequences - http://www.mothur.org/forum/viewtopic.php?f=5&t=402&sid=22d323d5316be7937cb6de9f3ea8cac4
- doubled the size of venn diagrams created.
- fixed bug with MPI Enabled version that would cause a malloc error if the number of seqs in your input file did not divide evenly between processes.
- http://www.mothur.org/forum/viewtopic.php?f=4&t=392&sid=54ce67de05b106db5435ba67e0583723, fixed bug that caused file mismatch issues because the read of qfile was based on sequence length in fasta file. It now reads the length directly from the qfile.
- fixed bug with classify.seqs that caused cutoff not to work if iters was not equal to 100.
- fixed bug with get.seqs that would cause the command to abort if both the input and output are redirected. - http://www.mothur.org/forum/viewtopic.php?f=4&t=398&sid=271fe0ebe8c7e8cf2a9ffe87e30d4cbb
- filter.seqs says it only uses 0 sequences to build filter
- you can now use the readline library with the mpi-enabled version - http://www.mothur.org/forum/viewtopic.php?f=4&t=396&sid=ed88315308710479c553039fdfd21d7e
- fixed bug with mothur's interface to blast, caused [NULL_Caption] FATAL ERROR.