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ChangeLog
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ChangeLog
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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.
Non-standard features already built-in include:
HMM-iteration (using HMMER for building an HMM) and guide-tree
iteration. On top of that HMM input works fine and
background-frequencies are added to the HHalign process.
Known issues: RNA/DNA alignment is considered buggy. Aligned
sequences have to be dealigned for HHalign to work properly.
The HMMER version message can be ignored if no HMM-iteration
was used.