hollalinux
/
slackbuilds
mirror of https://github.com/SlackBuildsOrg/slackbuilds.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

academic/seaview: Updated for version 4.3.4. 

Signed-off-by: dsomero <xgizzmo@slackbuilds.org>
This commit is contained in:
Petar Petrov 2012-06-30 11:59:43 -04:00 committed by dsomero
parent 344022d9c3
commit 45b68fd192
3 changed files with 29 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
academic/seaview/README
View File

@ -1,32 +1,32 @@
SeaView is a multiplatform, graphical user interface for multiple
SeaView is a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny. Important features are:
1) SeaView reads and writes various file formats (NEXUS, MSF,
CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences
1) SeaView reads and writes various file formats (NEXUS, MSF,
CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences
and of phylogenetic trees.
2) SeaView drives programs muscle or clustalw for multiple sequence
alignment, and also allows to use any external alignment algorithm
2) SeaView drives programs muscle or clustalw for multiple sequence
alignment, and also allows to use any external alignment algorithm
able to read and write FASTA-formatted files.
3) Seaview drives the Gblocks program to select blocks of
3) Seaview drives the Gblocks program to select blocks of
evolutionarily conserved sites.
4) SeaView computes phylogenetic trees by
a) parsimony, using PHYLIP's dnapars/protpars algorithm,
b) distance, with NJ or BioNJ algorithms on a variety of
b) distance, with NJ or BioNJ algorithms on a variety of
evolutionary distances,
c) maximum likelihood, driving program PhyML 3.0.
5) SeaView draws phylogenetic trees on screen, PDF or PostScript files
6) SeaView allows to download sequences from EMBL/GenBank/UniProt
6) SeaView allows to download sequences from EMBL/GenBank/UniProt
using the Internet.
For details and citation:
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224.
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224.
This requires fltk as a build dependency, but you also need clustalw,
Gblocks, PhyML, and muscle, all of which SeaView drives.
This requires fltk13. You will also need clustalw, Gblocks, PhyML, and
muscle, all of which SeaView drives.

10
academic/seaview/seaview.SlackBuild
View File

@ -24,8 +24,8 @@
# Thanks to Niels Horn for correcting the CFLAGS.
PRGNAM=seaview
VERSION=${VERSION:-4.3.3}
PRGNAM=seaview
VERSION=${VERSION:-4.3.4}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@ -40,7 +40,7 @@ fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
@ -73,6 +73,10 @@ find . \
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" Makefile
sed -i "14 c FLTK = /usr/include/fltk13" Makefile
sed -i "s:#IFLTK:IFLTK:" Makefile
sed -i "18 c LFLTK = -L/usr/lib${LIBDIRSUFFIX}/fltk13" Makefile
sed -i "28 a LDFLAGS= -Wl,--rpath,/usr/lib${LIBDIRSUFFIX}/fltk13" Makefile
# Point to the correct documentation path and phyml executable name
sed -i "s:#HELPFILE:HELPFILE:" Makefile

8
academic/seaview/seaview.info
View File

@ -1,10 +1,10 @@
PRGNAM="seaview"
VERSION="4.3.3"
VERSION="4.3.4"
HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.3.tar.gz"
MD5SUM="bee7f73988777721d7596535df8c2594"
DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.4.tar.gz"
MD5SUM="78098f9ea74655edbf8c8dae1d296340"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
MAINTAINER="Petar Petrov"
EMAIL="ppetrov@paju.oulu.fi"
APPROVED="rworkman"
APPROVED="dsomero"