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Committer: Bazaar Package Importer
Author(s): Charles Plessy
Date: 2006-08-05 09:57:27 UTC
mfrom: (2.1.2 etch)
Revision ID: james.westby@ubuntu.com-20060805095727-d9g347b21yl1bxbq

Tags: 3.60-1

http://bugs.debian.org/361742

* New upstram release (Closes: Bug#361742).
* New maintainers email addresses.

files added:
bittraceback.cpp

drawtree.cpp

glbalign352.cpp

muscle.cpp

muscleout.cpp

nwdasimple.cpp

nwdasimple2.cpp

nwdasmall.cpp

nwrec.cpp

nwsmall.cpp

objscoreda.cpp

outweights.cpp

physeq.cpp

profdb.cpp

readmx.cpp

refinew.cpp

scoregaps.cpp

scorepp.cpp

stabilize.cpp

subfam.cpp

subfams.cpp

termgaps.cpp

writescorefile.cpp

files removed:
scoremx.cpp

files modified:
Makefile

aligngivenpath.cpp

aligntwomsas.cpp

aligntwoprofs.cpp

alpha.cpp

alpha.h

anchors.cpp

debian/README.Debian

debian/changelog

debian/control

debian/copyright

debian/manpage.xml

diffobjscore.cpp

domuscle.cpp

dosp.cpp

dpreglist.cpp

enums.h

estring.cpp

fasta2.cpp

fastdist.cpp

fastdistmafft.cpp

fastdistnuc.cpp

fastscorepath2.cpp

finddiagsn.cpp

glbalign.cpp

glbaligndiag.cpp

glbalignle.cpp

glbalignsimple.cpp

glbalignspn.cpp

glbalndimer.cpp

globalslinux.cpp

henikoffweight.cpp

local.cpp

main.cpp

makerootmsa.cpp

makerootmsab.cpp

mhack.cpp

msa.cpp

msa.h

msa2.cpp

msadistkimura.cpp

msf.cpp

muscle.h

objscore.cpp

objscore.h

objscore2.cpp

options.cpp

params.cpp

params.h

phyfromfile.cpp

posgap.cpp

ppscore.cpp

profile.cpp

profile.h

profilefrommsa.cpp

progalign.cpp

progress.cpp

progressivealign.cpp

realigndiffse.cpp

refine.cpp

refinehoriz.cpp

refinetreee.cpp

savebest.cpp

seq.cpp

seqvect.cpp

seqvect.h

sw.cpp

textfile.cpp

textfile.h

types.h

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added added

removed removed

enums.h

s(ALPHA)

c(ALPHA, Amino)

c(ALPHA, Nucleo)

c(ALPHA, DNA)

c(ALPHA, RNA)

e(ALPHA)

s(SEQTYPE)

c(SEQTYPE, Protein)

c(SEQTYPE, Nucleo)

c(SEQTYPE, DNA)

c(SEQTYPE, RNA)

c(SEQTYPE, Auto)

e(SEQTYPE)

c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise

e(OBJSCORE)

s(TERMGAPS)

c(TERMGAPS, Full)

c(TERMGAPS, Half)

c(TERMGAPS, Ext)

e(TERMGAPS)

#undef s

#undef c

#undef e

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