New upstream version 36.3.8g (c1a8a345) · Commits · Debian Med / fasta3

README

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		[This file has been replaced by README.md]

		December, 2017

		The most up-to-date version information on FASTA versions is available
		in README.md and doc/readme.v36 .

		July, 2015

		This version of the FASTA programs is fasta-36.3.8. Since March, 2011

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		@@ -12,9 +12,26 @@ includes programs for aligning translated DNA sequences against
		proteins (`fastx`, `fasty` are equivalent to `blastx`, `tfastx`,
		`tfasty` are similar to `tblastn`).

		####September, 2016
		####December, 2017
		The current FASTA version is fasta-36.3.8f, Dec. 2017

		The statistics routines for normally distributed scores (ggsearch36,
		glsearch36) are more robust to very low E()-value thresholds.

		####Sept, 2017
		The current FASTA version is fasta-36.3.8f, Sept. 2017

		If the -S option is used and a query sequence has no upper case
		letters, it is re-read with lower-case letters converted to upper-case.

		The current FASTA version is fasta-36.3.8e.
		####May, 2017
		The current FASTA version is fasta-36.3.8f, May. 2017

		Various bugs in sub-alignment scoring corrected and support for the
		EBI SP:GSTM1_HUMAN P09488 added. The format for the $SRCH_URL and
		$SRCH_URL2 format strings has changed to enable pairwise alignment.

		####September, 2016

		The fasta-36.3.6e version includes a new directory, `psisearch2`, with
		scripts to run iterative PSSM (PSI-BLAST or SSEARCH36) searches using

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		@@ -6,7 +6,7 @@ Changes in fasta-36.3.8d released 13-April-2016:

		1. Various bug fixes to `pssm_asn_subs.c` that avoid coredumps when
		reading NCBI PSSM ASN.1 binary files. `pssm_asn_subs.c` can now read
		UUPACAA sequences.
		IUPACAA sequences.

		2. default gap penalties for VT40 (from -14/-2 to -13/-1), VT80 (from
		-14/-2 to -11/-1), and VT120 (from -10/-1 to 11/-1) have changed

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		## The FASTA package - protein and DNA sequence similarity searching and alignment programs

		Changes in fasta-36.3.8f released 31-Dec-2017

		1. (December, 2017) -- Make statistical thresholds more robust for
		small E()-values with normally distributed scores (ggsearch36,
		glsearch36).

		2. (September, 2017) Treat all lower-case queries as uppercase with -S option.

		3. (May, 2017) Improvements/fixes to sub-alignment scoring strategies.

		4. Improvements/fixes to psisearch2 scripts.

		For more detailed information, see `doc/readme.v36`.

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