MARCH 19, 2009
This is the standalone version of HaMStR v1

You need to download and install the tar-file containing the newest release of hamstrsearch_local.
Unpack the tar-archive and follow the installation guidelines in
the README file. 

This distribution comes by default with the modelorganisms core-ortholog set.
Hence the large file size. If you whish to use only your own core-orthologs
you may choose to download the hamstrsearch_local-bare.v1.0.tar.gz. This contains
only the data to perform the tests for proper installation of hamstrseach_local.

A number of additional core-ortholog sets can be downloaded from the core-ortholog
directory. Unpack the tar-archive and follow the instruction in the README file.
We will now and then add new core-ortholog sets to this directory.

For questions and comments please email ingo.ebersberger@univie.ac.at

New Releases:
HaMStR v1.1	May 07, 2009	Bug fix
HaMStR v1.2	June 09, 2009	Modification of the script to translate EST sequences (translate.pl). A check for uniqueness of the sequence identifiers is now implemented.
HaMStR v1.3	June 29, 2009	Bug fix in the output of the CDS information. 
HaMStR v1.4	Aug 28, 2009	Bug fix in the genewise CDS prediction. This is a critical update and removes the problem of short sequences in the HaMStr output. From this version on, I provide also a version of hamstrsearch_local that uses hmmsearch of the hmm-3.0b2 release.
HaMStR v4	Nov 03, 2010	This is a new version of HaMStR. It now runs only with hmmsearch from the HMMER 3 suite. It provides a number of new features like strict searches and relaxed searches for orthologs. Note, that this version of hamstr is not compatible with pHMMs that have been built with the hmmbuild of HMMER 2. Contact me if you have questions.
HaMStR v6	Mar 11, 2011	I have now fixed the problem that HaMStR had with sequence_files where the individual sequences were interupted by linebreaks. HaMStR now runs the script nentferner.pl on the sequence_file first, stores the modified sequences separately and uses them for the analysis. Moreover, the order of the fields in the hamstr output file no longer changes depending on whether or not you use the -representative flag. 
HaMStR v7	May 20, 2011	I fixed a bug in the predictORF sub-routine. The grep for the EST sequence in the sub-routine predictORF received also a hit when the search pattern was only a substring of the EST sequence identifier. In some cases the wrong EST was then used to predict the ORF. This has been fixed.
HaMStR v8	Aug 16, 2011	I added two options to HaMStR: 
			1) Option -rbh accepts only then a protein as ortholog if it is best hit in both the pHMM based search AND in the reciprocal BLAST search against the reference taxon. By default it is sufficient that only the BLAST hit is a Best Blast Hit.
			1) Option -longhead (experimental) allows the use of longer sequence headers that include also white-spaces. This is a bit tricky since genewise truncates sequence header. I suggest to use this option only with care.