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Mothur v.1.7.0

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Revision as of 19:26, 23 November 2009 by Westcott (Talk | contribs)

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  • get.listcount command - Ever wonder after a cluster what sequences are in those bins?? Thanks to a user request, here is the solution. Given a list file, this command will output a .otu file for each distance specified containing the bin number and a list of the sequences in that bin.
  • updated read.otu command - you can now use the groups parameter to specify which groups you would like to use. If you provide groups mothur will generate a .rabund file for each group, a .shared file containing only those groups and a new group file containing only the sequences in the groups you specified.
  • hcluster command - clusters distance files of any size. It's slower than the cluster command, which stores the distance in RAM to increase performance, so if you can fit your file in RAM use cluster.
  • classify.seqs command - classifies sequences using the knn or bayesian methods.
  • phylotype command - creates .list, .rabund and .sabund files from a taxonomy file.
  • added all parameter to the summary.shared and collect.shared commands. The sharedchao and sharedsobs calculators not only give you the pairwise richness estimates for your groups, but also estimate the combined richness of all your groups. The all parameter allows you to specify whether or not you want mothur to find this combined group estimate. By default it is set to true, but if you have a large number of groups the combined estimate may cause you to run out of ram, to avoid this problem and yet still get the pairwise richness estimates set all to false.
  • added qtrim parameter to trim.seqs command. By default qtrim is false, meaning if a sequence falls below the qthreshold it will go to the scrap file. If qtrim is set to true and a sequence falls below the qthreshold, it will be trimmed and put in the trim file.