2020年7月 – 学术咖

PHAST：Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

Major PHAST programs：

phastCons: Conservation scoring and identification of conserved elements
phyloFit: Fitting of phylogenetic models to aligned DNA sequences
phyloP: Computation of p-values for conservation or acceleration, either lineage-specific or across all branches
phastOdds: Log-odds scoring for phylogenetic models or phylo-HMMs
exoniphy: Phylogenetic exon prediction
dless: Prediction of elements under lineage-specific selection
prequel: Probabilistic reconstruction of ancestral sequences
phastBias: Identification of GC-biased gene conversion using a phylo-HMM

安装PHAST：

wget -c http://www.netlib.org/clapack/clapack.tgz
tar -xvzf clapack.tgz
cd CLAPACK-3.2.1
cp make.inc.example make.inc && make f2clib && make blaslib && make lib
wget -c http://compgen.cshl.edu/phast/downloads/phast.v1_5.tgz
tar zxf phast.v1_5.tgz
cd phast/src/
make CLAPACKPATH=/opt/biosoft/CLAPACK-3.2.1
echo 'PATH=$PATH:/opt/biosoft/phast/bin' >> ~/.bashrc
source ~/.bashrc

MCScanX：perl -e 'while (<>) { if (m/^(\S+)\t.*\tgene\t(\d+)\t(\d+).*ID=(darer\d+)/) { print "$1\t$4\t$2\t$3\n" } }' darer.genome.gff3 > darer.gff jcvi：perl -e 'while (<>) { if (m/^(\S+)\t.*\tgene\t(\d+)\t(\d+)\t(\S+)\t(\S+).*ID=(darer\d+)/) { print "$1\t$2\t$3\t$6\t$4\t$5\n" } }' darer.genome.gff3 > zebr.bed

cat darer.gff gc.gff > all.gff cat darer.pep.fasta gc.pep.fasta > all.pep.fasta makeblastdb -in all.pep.fasta -dbtype prot -title all -parse_seqids -out all -logfile all.log blast.pl blastp all all.pep.fasta 1e-10 160 blast 6 mkdir MCScanx mv ../blast.tab all.blast mv ../all.gff ./ MCScanX all cd .. mkdir jcvi && cd jcvi mv ../*.bed ./ mv ../darer.pep.fasta darer.pep mv ../gc.pep.fasta gc.pep python -m jcvi.compara.catalog ortholog --dbtype prot --no_strip_names darer gc python -m jcvi.compara.synteny screen --minspan=30 --simple darer.gc.anchors darer.gc.anchors.new

月份：2020年7月

PHAST安装使用

使用MCScanX和JCVI共线性区块分析