From f2352ec41227dba528c64573fa62ac287a292a58 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 11 Sep 2023 15:05:54 +0700 Subject: academic/FastTree: Added (Infers approximately-ML phylogenetic). Signed-off-by: Willy Sudiarto Raharjo --- academic/FastTree/FastTree.SlackBuild | 85 +++++++++++++++++++++++++++++++++++ academic/FastTree/FastTree.info | 10 +++++ academic/FastTree/README | 17 +++++++ academic/FastTree/References | 14 ++++++ academic/FastTree/slack-desc | 19 ++++++++ 5 files changed, 145 insertions(+) create mode 100644 academic/FastTree/FastTree.SlackBuild create mode 100644 academic/FastTree/FastTree.info create mode 100644 academic/FastTree/README create mode 100644 academic/FastTree/References create mode 100644 academic/FastTree/slack-desc (limited to 'academic/FastTree') diff --git a/academic/FastTree/FastTree.SlackBuild b/academic/FastTree/FastTree.SlackBuild new file mode 100644 index 000000000000..6c954faf8dc7 --- /dev/null +++ b/academic/FastTree/FastTree.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/bash + +# Slackware build script for FastTree + +# Copyright 2023 Petar Petrov, slackalaxy at gmail dot com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=FastTree +VERSION=${VERSION:-2.1.11} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +cp $CWD/$PRGNAM.c . +gcc $SLKCFLAGS -o FastTree FastTree.c -lm +install -D -m755 FastTree $PKG/usr/bin/FastTree + +cd $PKG/usr/bin +ln -s FastTree fasttree + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/FastTree/FastTree.info b/academic/FastTree/FastTree.info new file mode 100644 index 000000000000..006113cf06b0 --- /dev/null +++ b/academic/FastTree/FastTree.info @@ -0,0 +1,10 @@ +PRGNAM="FastTree" +VERSION="2.1.11" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +DOWNLOAD="http://www.microbesonline.org/fasttree/FastTree.c" +MD5SUM="83bf082910e1d704e1b1b35f5e263ece" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/FastTree/README b/academic/FastTree/README new file mode 100644 index 000000000000..4398c4f34390 --- /dev/null +++ b/academic/FastTree/README @@ -0,0 +1,17 @@ +FastTree infers approximately-maximum-likelihood phylogenetic trees from +alignments of nucleotide or protein sequences. FastTree can handle +alignments with up to a million of sequences in a reasonable amount of +time and memory. For large alignments, FastTree is 100-1,000 times +faster than PhyML 3.0 or RAxML 7. FastTree is open-source software. + +FastTree is more accurate than PhyML 3 with default settings, and much +more accurate than the distance-matrix methods that are traditionally +used for large alignments. FastTree uses the Jukes-Cantor or generalized +time-reversible (GTR) models of nucleotide evolution and the JTT +(Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and +Gascuel 2008) models of amino acid evolution. To account for the varying +rates of evolution across sites, FastTree uses a single rate for each +site (the "CAT" approximation). To quickly estimate the reliability of +each split in the tree, FastTree computes local support values with the +Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local +supports"). diff --git a/academic/FastTree/References b/academic/FastTree/References new file mode 100644 index 000000000000..01aef49abf6d --- /dev/null +++ b/academic/FastTree/References @@ -0,0 +1,14 @@ +These papers describe FastTree: the first paper describes FastTree 1.0, +and the second paper describes heuristic minimum-evolution SPR moves, +maximum-likelihood NNIs, and SH-like local supports. We have also +eliminated the O(N2) steps in the neighbor-joining phase, and +implemented maximum-likelihood NNI moves and SH-like supports (see the +ChangeLog). + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing +Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. +Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077. + +Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- +Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, +5(3):e9490. doi:10.1371/journal.pone.0009490. diff --git a/academic/FastTree/slack-desc b/academic/FastTree/slack-desc new file mode 100644 index 000000000000..e74540e239fa --- /dev/null +++ b/academic/FastTree/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +FastTree: FastTree (Infers approximately-ML phylogenetic trees) +FastTree: +FastTree: FastTree infers approximately-maximum-likelihood phylogenetic trees +FastTree: from alignments of nucleotide or protein sequences. FastTree can +FastTree: handle alignments with up to a million of sequences in a reasonable +FastTree: amount of time and memory. +FastTree: +FastTree: http://www.microbesonline.org/fasttree/ +FastTree: +FastTree: +FastTree: -- cgit v1.2.3