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Difference between revisions of "Mothur v.1.4.0"

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(Minor updates)
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* the heatmap command is now called [[heatmap.bin]].
* the heatmap command is now called [[heatmap.bin]].
* modified how the [[help]] command is called
* modified how the [[help]] command is called
* can now enter a string of commands separated by ';' and starting with '#', when executing mothur.
  example: ./mothur "#read.otu(list=amazon.fn.list);collect.single();rarefaction.single();heatmap.bin();quit();"
==Bug fixes==
==Bug fixes==

Revision as of 12:05, 18 June 2009

Major updates

  • align.seqs - generates an alignment to a user-supplied template alignment database [pds]
  • 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]
  • heatmap.sim - creates a heatmap based on groups similiarity.
  • get.rabund - outputs an rabund file
  • get.sabund - outputs an sabund file
  • trim.seqs - trims and culls sequences based on user-defined criteria, barcodes, and primers
  • merge.files - concatenates a list of files

Minor updates

  • tree.shared command now allows you to input a 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.
  • 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.
  • modified how the help command is called
  • can now enter a string of commands separated by ';' and starting with '#', when executing mothur.
 example: ./mothur "#read.otu(list=amazon.fn.list);collect.single();rarefaction.single();heatmap.bin();quit();"

Bug fixes

  • 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 unique.seqs 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.