-2010-06-17 Release 0.0.1 (Dubliniensis)
+2016-12-20 Release 1.2.4 (AndreaGiacomo, r317)
+
+ - made code gcc-6 compliant
+
+ (no new command-line flags)
+
+2016-07-20 Release 1.2.3 (AndreaGiacomo, r313)
+
+ - fixed consensus line in ClustalW format, 'H' in NHQK not recognised as strong (bug in Squid)
+
+ (no new command-line flags)
+
+2016-07-01 Release 1.2.2 (AndreaGiacomo, r310)
+
+ - fixed a memory leak in hhalign
+ - parallelised hhalign
+ - increased MAC-RAM default from 2GB to 8GB
+
+ (no new command-line flags)
+
+2014-02-28 Release 1.2.1 (AndreaGiacomo, r292)
+
+ - corrected Clustal format consensus line
+ - label justification (multi-bit)
+
+2013-06-12 Release 1.2.0 (AndreaGiacomo, r284)
+
+ --is-profile disable check if profile, force profile (default no)
+ --use-kimura use Kimura distance correction for aligned sequences (default no)
+ --percent-id convert distances into percent identities (default no)
+
+ fixed bug in --output-order=tree-order for pair-wise alignment
+
+ Kimura distance correction no longer default for protein
+
+ fixed bug in Viterbi algorithm (predominantly affected long nucleotide but also protein, to lesser extent)
+
+ Viterbi is less (~10x) memory hungry than MAC but still scales quadratically with length:
+
+ 2GB of RAM (ClustalO default) can align sequences of 6.5k residues with MAC and 18k with Viterbi
+
+ 8GB of RAM (EBI limit) can align sequences of 12.5k residues with MAC and 37k with Viterbi
+
+ A Viterbi alignment of sequences of 100k residues will require 59GB of RAM
+
+
+2013-05-16 Release 1.1.1 (r281)
+
+ --cluster-size=<n> soft maximum of sequences in sub-clusters
+ --clustering-out=<file> Clustering output file
+ --residuenumber, --resno in Clustal format print residue numbers (default no)
+ --wrap=<n> number of residues before line-wrap in output
+ --output-order={input-order,tree-order} MSA output order like in input/guide-tree
+
+ turned off Kimura correction for DNA/RNA
+
+ enable distance matrix output after initial mBed but subsequent full distance calculation
+
+ enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)
+
+ longer sequence labels
+
+2012-04-25 Release 1.1.0 (FilumVitae, r275)
+
+ DNA and RNA support now added. Sequence type can be specified manually
+ using --seqtype={Protein|DNA|RNA}
+
+2012-03-27 Release 1.0.4 (r273)
+
+ zipped input now supported
+
+2011-09-07 Release 1.0.3 (r263)
+
+Bugs fixed:
+
+ input failed if first line in fasta file was empty
+
+ input failed if Clustal formatted file had trailing residue numbers
+
+ '*' character was causing problems, did not get filtered out by squid
+
+ --outfmt=fasta was not recognized
+
+ '~' gap characters were not recognized in MSF format
+
+ amended README re sequence/profile alignment
+
+ disallowed empty sequences
+
+ doxygen documentation fixes and fix of API example
+
+ introduced MAC-RAM flag to set amount of RAM given to MAC (in MB)
+
+2011-06-23 Release 1.0.2
+
+2011-06-17 Release 1.0.0 (DeshilHollesEamus, r250)
+
+2011-04-14 Release 0.2.0 (IbiMeVidebunt, r238)
+
+2011-03-23 Release 0.1.1 (OppidumLeonis, r224)
+
+2011-02-22 Release 0.1.0 (OppidumLeonis, r200)
+
+2010-08-10 Release 0.0.3 (Thamesis, r120)
+
+2010-06-17 Release 0.0.1 (Dubliniensis, r81)
First "release" as program has been able for a while to perform
all basic tasks without problems.
git://source.jalview.org / jabaws.git / blobdiff