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Difference between revisions of "Mothur v.1.10.0"

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(Feature updates)
 
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These will be available in the next version of mothur.  Stay tuned for a release in May 2010.
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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. 
  
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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!
  
==New commands==
 
  
  
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==New commands==
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* added [[set.logfile]] command - allows user to set logfile name and/or append the log to an existing file
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* added [[phylo.diversity]] command -  [[phylogenetic diversity]]
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* added [[make.group]] command - http://www.mothur.org/forum/viewtopic.php?f=3&t=385&sid=6260346b9aab4bf74e20f667fd135cb4
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* added [[chop.seqs]] command - http://www.mothur.org/forum/viewtopic.php?f=3&t=399&sid=ecc7b9a7e046fb48f5a5345713ef3fd2
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* added [[clearcut]] command -  wrapper for [http://bioinformatics.hungry.com/clearcut/ clearcut]
  
 
==Feature updates==
 
==Feature updates==
 
* 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.
 
* 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.
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* made taxonomy static between runs
 
* speed comparison between our classify.seqs with bayesian and the RDPs.  Have received reports that ours is much slower.
 
* 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
 
* added name option for [[phylotype]] command
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* parallelized [[screen.seqs]] - made it MPI Enabled
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* parallelized [[trim.seqs]]
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* added tdiffs, bdiffs and pdiffs parameters to [[trim.seqs]] command
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* 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.
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* 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.
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* [[remove.seqs]] can remove sequences from multiple files at once.
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* mothur now recognizes ~, so you can enter filenames like ~/desktop/myFile.fasta, or set.dir(output=~)
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* added 3 constructors to sequence class that just fill unaligned field to save space when we don't need an aligned sequence.
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* made freq a percentage of number of sequences - http://www.mothur.org/forum/viewtopic.php?f=5&t=402&sid=22d323d5316be7937cb6de9f3ea8cac4
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* doubled the size of venn diagrams created.
  
 
==Bug fixes==
 
==Bug fixes==
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* 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.
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* 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.
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* fixed bug with [[classify.seqs]] that caused cutoff not to work if iters was not equal to 100.
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* 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
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* [[filter.seqs]] says it only uses 0 sequences to build filter
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* 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
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* fixed bug with mothur's interface to blast, caused [NULL_Caption] FATAL ERROR.

Latest revision as of 16:38, 17 May 2010

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!


New commands

Feature updates

Bug fixes