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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| ReadMe-ReleaseNote-v13.2.2a.txt | 2014-08-07 | 2.2 kB | |
| hamstr.v13.2.bin.tar.gz | 2014-02-16 | 361.7 kB | |
| ReadMe-ReleaseNote-v13.2.txt | 2014-02-16 | 1.4 kB | |
| hamstr_v13.1c.bin.tar.gz | 2014-02-11 | 23.9 kB | |
| ReadMe-ReleaseNote-v13.1c.txt | 2014-02-11 | 1.3 kB | |
| ReadMe-ReleaseNote-v13.1b.txt | 2014-02-11 | 3.5 kB | |
| Totals: 6 Items | 394.0 kB | 0 | |
Release note for HaMStR v. 13.2.2a April 2nd, 214 BUG FIX (Minor) Updating of the variable $runublast upon configuring with the ublast option did not work. HaMStR when issued with the -ublast option died with the message 'hamstr has been configured with the -noublast option'. This has been fixed March 16th, 2014 This is an extension of HaMStR bringing the option to speed up the ortholog search by at least 50%. You will have now the option to choose ublast rather than conventional BLAST for the reverse search. NEW (13.2.2) BUG FIX 1) Corrected a bug resulting in translating all transcripts in the same frame. MODIFICATIONS 1) In the determineRef subroutine the sorting of the alignment start, end and alignment score is now done internally RECENT CHANGES (13.2.1) BUG FIX 1) In some functions a call to grep was hard coded and did not make use of the global variable $grepprog. For users running on MAC OS this can result in an unwanted call of BSD grep rather than GNU grep causing a problem in the re-blast routine. NEW FEATURES 1) I have added the option -ublast and -accel that can be used to invoke the ublast search instead of the default BLAST. Note, that you will have to download the usearch software from http://drive5.com/usearch/ prior to configuring HaMStR. 2) Bug fix: I dedected a bug in the HaMStR v13.1c resulting in incorrectly formatted output. This has been corrected now. ALPHA STATUS 1) Speed-up: The first step has been done. Still, a more efficient IO management minimizing file system access is required. 2) Some of the new features have not been tested exhaustively, although I tried my best. If you are unsure and prefer to stick with the 'old' part of HaMStR simply set the option -representative. In the upcoming weeks I will try to evaluate the novel features more thoroughly. Any comments are of course highly welcome. 3) A HaMStR Gui in an alpha version is now available and you can contact me for a test version. TO DO 1) Iterative compilation of core ortholog groups using individual query sequences as start Thanks for using HaMStR and drop me a line if you encounter any difficulties or problems.