diff options
Diffstat (limited to 'academic/seaview')
| -rw-r--r-- | academic/seaview/README | 41 | ||||
| -rw-r--r-- | academic/seaview/seaview.SlackBuild | 12 | ||||
| -rw-r--r-- | academic/seaview/seaview.info | 8 |
3 files changed, 28 insertions, 33 deletions
diff --git a/academic/seaview/README b/academic/seaview/README index 70a537171c295..e72249f563409 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -1,28 +1,23 @@ SeaView is a multiplatform, graphical user interface for multiple -sequence alignment and molecular phylogeny. Important features are: +sequence alignment and molecular phylogeny. Features: -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 Clustal Omega (clustalo) 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 - 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 - evolutionary distances, - c) maximum likelihood, driving program PhyML - -5) SeaView prints and draws phylogenetic trees on screen, SVG, PDF or - PostScript files. - -6) SeaView allows to download sequences from EMBL/GenBank/UniProt - using the Internet. +- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, + PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic + trees. +- Drives programs muscle or Clustal Omega for multiple sequence + alignment, and also allows to use any external alignment + algorithm able to read and write FASTA-formatted files. +- Drives the Gblocks program to select blocks of evolutionarily + conserved sites. +- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars / + protpars algorithm, distance, with NJ or BioNJ algorithms on a variety + of evolutionary distances, maximum likelihood, driving program PhyML +- Can use the Transfer Bootstrap Expectation method to compute the + bootstrap support of PhyML and distance trees. +- Uses the Treerecs method to reconcile gene and species trees. +- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript + files. +- Allows to download sequences from EMBL / GenBank / UniProt. For details and citation: Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 2def34de149cb..522170872cc8a 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for seaview -# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,7 +26,7 @@ # Thanks to developer Dr. Manolo Gouy for all his help. PRGNAM=seaview -VERSION=${VERSION:-4.7} +VERSION=${VERSION:-5.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -67,10 +67,10 @@ tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz cd $PRGNAM chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index 116ac4c44e256..fc329f3fd3584 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,10 +1,10 @@ PRGNAM="seaview" -VERSION="4.7" +VERSION="5.0" HOMEPAGE="http://doua.prabi.fr/software/seaview/" -DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.7.tar.gz" -MD5SUM="9c1ee28e7f870b76991de17b22d7dfcb" +DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.tar.gz" +MD5SUM="d9f1a97672efb3fd24850cf542326915" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle" +REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle treerecs" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" |