New SLiMSuite, SeqSuite and RJESuite downloads available

Just in time for Christmas, new releases of all the downloads are available at the Edwards Lab software page. Documentation is still lagging behind but will hopefully catch up (along with a bit of an overhaul of this blog). Questions welcome in the meantime.

In addition to QSLiMFinder 1.4, the biggest change this release is probably the upgrade of GOPHER. Version 3.x features improved organisation of output files for queries from different species in addition to a capacity to have several different multiple alignment programs run on the same orthologue sets. See the website for more info.

Updates since last release:

• gopher: Created.
→ Version 3.0: See archived GOPHER 1.9 and gopher_V2 2.9 for history and obselete options.
→ Version 3.0: Added organise=T/F and gopherdir=PATH for improved file organisation. Tightened savespace.
→ Version 3.0: Added compfilter=T/F for improved complexity filter and composition statistics control for *initial* BLAST.
→ Version 3.0: Changed default tree extension to *.nwk for compatibility with MEGA. Deleted _phosAlign() method.
→ Version 3.0: Added orthology ID option and alignment program to customise output further.
→ Version 3.1: Added full reciprocal best hit method. (fullrbh=T/F)

• gopher_V2: Updated from Version 2.8.
→ Version 2.9: Deleted oldStigg() method. Added simple Reciprocal Best Hit orthology prediction.

• qslimfinder: Updated from Version 1.2.
→ Version 1.3: Updated the output for Max/Min filtering and the pickup options.
→ Version 1.4: Added additional dictionary and list to store Query dimers and SLiMs for motif space calculations.
→ Version 1.4: Added qexact=T/F option for calculating Exact Query motif space (True) or estimating from dimers (False).

• slimfinder: Updated from Version 4.2.
→ Version 4.3: Updated the output for Max/Min filtering and the pickup options. Removed TempMaxSetting.
→ Version 4.4: Modified to work with GOPHER V3.0.

• rje: Updated from Version 4.3.
→ Version 4.4: Added lineFromIndex(target,file,re_index='^(\S+)\s',sortunique=False,xreplace=True).

• rje_seq: Updated from Version 3.13.
→ Version 3.14: Added CLUSTAL Omega alignment program ['clustalo']
→ Version 3.15: Added PAGAN alignment program ['pagan'] and (hopefully) fixed minor Windows fastacmd bug.

• rje_sequence: Updated from Version 2.1.
→ Version 2.2: Added more yeast species.

• rje_slimcalc: Updated from Version 0.4.
→ Version 0.5: Altered to use GOPHER V3 and handle nested alignment directories.

• rje_slimlist: Updated from Version 1.0.
→ Version 1.1: Modified to work with GOPHER V3.0 for alignments.