Commit 071874f3 authored by Andreas Tille's avatar Andreas Tille

New upstream version 3.69.660

parent 8ae58226
This is an EMBOSS port of the PHYLIP 3.69 package from Joe Felsenstein
at the University of Washington.
The original version of PHYLIP os available from
http://evolution.gs.washington.edu/phylip/software.html
The EMBOSS port involves replacing the user interface with an EMBOSS
ACD file and using EMBOSS to parse the input data. Once data has been
loaded, all the algorithms and outputs use the original PHYLIP code.
In a future release we may add EMBOSS output code so that the user has
a choice of output formats.
The EMBOSS versions of the programs all have 'f' added to the start of
the name so you can run native PHYLIP on the same system to check your
results.
Copyright Notice for PHYLIP 3.69
The following copyright notice is intended to cover all source code, all
documentation, and all executable programs of the PHYLIP package.
(c) Copyright 1980-2008. University of Washington. All rights
reserved. Permission is granted to reproduce, perform, and modify
these programs and documentation files. Permission is granted to
distribute or provide access to these programs provided that this
copyright notice is not removed, the programs are not integrated with
or called by any product or service that generates revenue, and that
your distribution of these documentation files and programs are free.
Any modified versions of these materials that are distributed or
accessible shall indicate that they are based on these programs.
Institutions of higher education are granted permission to distribute
this material to their students and staff for a fee to recover
distribution costs. Permission requests for any other distribution of
these program should be directed to license(at)u.washington.edu
Release 3.69 update July 2011
Changed -thresh to -dothreshold and -gamma to -gammatype to avoid
qualifier name clashes with stricter ACD validation.
The *boot applications reported the status of some boolean options
and printed "Done" at the end. Removed the boolean reports and now
only print "Done" unless -noprogress is set to allow piping.
Release 3.69
Updated all code to include the changes in phylip 3.69.
Release 3.68
Updated all code to include the changes in phylip 3.68.
fdnadist no longer writes a blank line at the end of the output.
fconsense writes trees with 2 decimal places.
A bug in fprotdist for scores of 100.0 is fixed.
Rearrangement messages are no longer printed by fpromlk.
fprotdist and fprotpars now write "Done" when completed.
Renamed fdrawgram qualifiers to make unambiguous names shorter:
xmarginray => xrayshade ymarginray => yrayshade for RayShade
output image size in pixels.
Removed unused fdrawtree qualifiers plotterpcl and plotterpcx.
Added 4 new plotter options for the additional resolutions
previously defined by plotterpcl and plotterpcx.
Renamed fdrawtree qualifiers to make unambiguous names shorter:
xmarginray => xrayshade; ymarginray => yrayshade for RayShade
output image size in pixels.
Release 3.67
Updated all code to phylip 3.67. The output of several programs has
changed - see the phylip release notes for details. Programs with
changed output are all the molecular clock algorithms : fcontml,
fdnaml, fdnamlk, proml, promlk, restml. ftreedist and ftreedistpair
branch score distance output has also changed in phylip 3.67
fontfile now works correctly in fdrawgram and fdrawtree. The
fontfile value must be a known phylip font in the data directory.
previewing with X11 was broken. Setting "none" for previewer no
longer prompts before plotting.
frestdist had a memory access error reported by valgrind. The same
error was found in the original phylip source, and fixed by
copying in code changes in phylip 3.66
fclique had an error reading the ancestors file. Results now agree
with those from the original phylip 3.6 code.
fdnamove had an internal overflow. Array chh[11] needed at least
one extra space.
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#
ACLOCAL_AMFLAGS = -I m4
SUBDIRS = src emboss_acd data emboss_doc
EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess
# tar to pick up the other directories
# then remove any CVS subdirectories
dist-hook:
tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS )
tar cBf - emboss_doc | ( cd $(distdir); tar xBf - ; cd emboss_doc; rm -rf CVS; rm -rf master)
tar cBf - doc | ( cd $(distdir); tar xBf - ; cd doc; rm -rf CVS )
tar cBf - include | ( cd $(distdir); tar xBf - ; cd include; rm -rf CVS )
tar cBf - data | ( cd $(distdir); tar xBf - ; cd data; rm -rf CVS )
tar cBf - test | ( cd $(distdir); tar xBf - ; cd test; rm -rf CVS)
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This is the EMBOSS integrated version of PHYLIP 3.69
If you require the original PHYLIP 3.69 distribution, you should
obtain it from the author, Joe Felsenstein, at
http://evolution.gs.washington.edu/phylip/software.html
This file records the steps involved in making PHYLIP 3.69 compatible
with EMBOSS as an EMBASSY package. The procedure is relatively simple,
compared to other packages, as PHYLIP has a nicely isolated user
interface and our main task is to write the ACD interface.
1. Make a new directory, and copy in the phylip source (src/
directory) and documentation (doc/ directory) files.
2. Move the include files (*.h) from src/ to include/
3. Create a configure.in file in the ./ directory
4. Create a Makefile.am file in the ./ src/ and emboss_acd/ directories
5. In src/Makefile.am use a prefix 'f' for every program. In this way
the original PHYLIP package can co-exist with the EMBASSY version,
and so can the EMBASSY PHYLIP 3.5 package, which used an 'e'
prefix. We can claim that the 'f' stands for 'PHYLIP' although
being the letter after 'e' is also a significant factor.
6. Add files in the emboss_acd directory (initially from the phylip
embassy package) with the 'f' prefix.
7. In include/phylip.h rename VERSION to ORIGINALVERSION as our new
./configure will define it. Put the same version (3.69) into
./configure
8. Looks like PHYLIP 3.69 has new library source code - these functions
were generally in the main program *.c files before. We add these as extra
sources in Makefile.am
9. PHYLIP 3.69 has programs we did not build in PHYLIP 3.5. This time,
we build them all (for now).
10. Put the ACD interface into each program:
(a) comment out with the existing getoptions function
put /* */ around it
put // on every line so we know it is changed
change /* */ to /# #/
(b) add an emboss_getoptions function in main (after "init()")
to initialise the same variables ad the original getoptions
and to use ajAcdGet calls
(c) use the modified openfile calls in the remaining code
11. Options are also defined in a set of functions in phylip.c
Replace these with calls to standard ACD options. EMBOSS
validation will catch any that are not defined in the ACD file.
12. Make sure we add ajExit() at the end of main to test for unused
ACD options and final debug output.
13. Use perl scriptsd to check for options in the source (prompts in
getoptions and calls to the phylip.c "init" functions. Compare
these to the ACD files from PHYLIP 3.5 and update accordingly.
14. Make test cases using the test data from the phylip doc/*.html
examples. Use these to test both phylip 3.69 and phylip 3.5 and
note any differences.
15. Some programs allow multiple input datasets. This means a
seqsetall ACD type which we don't have yet. Set the maximum to 1
for these, but allow unlimited datasets where the same option
-datasets refers to a weight file which is a simple infile that we
let PHYLIP read.
16. Convert printf and exxit(-1) to use ajErr for the message and make
exxit(-1) call ajExitBad()
17. Programs end with printf("Done") - and other progress reports.
Comment them out.
18. Made new ACD data types for Dist, Freq, Properties, Tree
and tried to read all their many file formats.
19. Made fcontrast work with the new style for frequency and tree
data. This meant parsing trees from strings instead of files (lots
of changes to phylip.c treeread onwards), although the frequency
part was (so far) pretty simple.
20. So remove the old functions that read files (all of them!)
Pass trees as char*
Carefully put Freq->Data into new arrays (in input order :-)
Keep ACD minimal for now.
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Makefile.in
Makefile
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pkgdata_DATA = font1 font2 font3 font4 font5 \
font6
pkgdatadir=$(prefix)/share/$(PACKAGE)/data/
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Source: embassy-phylip
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@debian.org>
Section: non-free/science
Priority: optional
Build-Depends: debhelper (>= 9),
autotools-dev,
libxaw7-dev,
emboss-lib (>= 6.6.0-1~),
emboss-lib (<< 6.6.1~),
libgd2-xpm-dev,
default-libmysqlclient-dev,
libpq-dev
Standards-Version: 3.9.8
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/embassy-phylip/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/embassy-phylip/trunk/
Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#PHYLIPNEW
XS-Autobuild: yes
Package: embassy-phylip
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
emboss-lib (>= 6.6.0-1~),
emboss-lib (<< 6.6.1~)
Description: EMBOSS conversions of the programs in the phylip package
This package is the adaptation of the PHYLIP package in which its
programs can operate with the biological sequence formats and databases
of the European Molecular Biology Open Software Suite (EMBOSS). The
software packages adapted for EMBOSS are called EMBASSY.
.
PHYLIP (the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). Methods that are available
in the package include parsimony, distance matrix, and likelihood
methods, including bootstrapping and consensus trees. Data types that
can be handled include molecular sequences, gene frequencies,
restriction sites and fragments, distance matrices, and discrete
characters.
.
The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them
from the original programs and avoid namespace conflict.
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ChangeLog
README
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version=3
ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-(.*).tar.gz
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