JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

[jabaws.git] / binaries / windows / clustalo / ChangeLog

diff --git a/binaries/windows/clustalo/ChangeLog b/binaries/windows/clustalo/ChangeLog
deleted file mode 100755 (executable)
index 1f4c740..0000000
--- a/binaries/windows/clustalo/ChangeLog
+++ /dev/null
@@ -1,100 +0,0 @@
-2016-07-01 Release 1.2.2 (AndreaGiacomo)
-
-       - fixed a memory leak in hhalign
-       - paralleised hhalign
-       - increased MAC-RAM default from 2GB to 8GB
-
-       (no new command-line flags)
-
-2014-02-28 Release 1.2.1 (AndreaGiacomo)
-
-       - corrected Clustal format consensus line
-       - label justification (multi-bit)
-       
-2013-06-12 Release 1.2.0 (AndreaGiacomo)
-
-       --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
-
-         --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
-
-   DNA and RNA support now added. Sequence type can be specified manually
-   using --seqtype={Protein|DNA|RNA}
-
-2012-03-27 Release 1.0.4
-
-   zipped input now supported
-
-2011-09-07 Release 1.0.3 
-
-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)
-
-2010-06-17 Release 0.0.1 (Dubliniensis)
-               
-               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.