Prodigal（基因預(yù)測）

sudo git clone https://github.com/hyattpd/Prodigal.git
cd Prodigal/
sudo make install
prodigal -i 77_bin.001.fasta -o 77_bin.001.gbk -a 77_bin.001.faa

RNAmmer (rRNA預(yù)測)

先安裝hmmer-2.2g

sudo wget http://eddylab.org/software/hmmer/hmmer-2.2g.tar.gz
tar zxvf hmmer-2.2g.tar.gz
cd hmmer-2.2g
./configure
make

下載http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer （需要edu郵箱）

#安裝
mkdir rnammer
cp sudo mv rnammer-1.2.src.tar.Z rnammer
cd rnammer
sudo tar zxvf rnammer-1.2.src.tar.Z
##然后進入rnammer修改部分地址
my $INSTALL_PATH = "/usr/cbs/bio/src/rnammer-1.2";
修改為my $INSTALL_PATH = "/home/llt/software/rnammer/";
HMMSEARCH_BINARY = "/usr/cbs/bio/bin/linux64/hmmsearch";
修改為$HMMSEARCH_BINARY = "/home/llt/software/hmmer-2.2g/binaries/hmmsearch";（兩處修改）
#使用
rnammer -S bac -m lsu,ssu,tsu -xml bin.xml -gff bin.gff -h bin.hmmreport < bin.fasta

barrnap (rRNA預(yù)測)

git clone https://github.com/tseemann/barrnap.git
cd barrnap/bin
/home/llt/software/barrnap/bin/barrnap --kingdom arc  --threads 4 33_bin.001.fasta  > 33_bin.001.rna.gff3

tRNAscan-SE (tRNA預(yù)測)

sudo wget http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
sudo tar zxvf trnascan-se-2.0.2.tar.gz
cd tRNAscan-SE-2.0/
sudo ./configure
sudo make
sudo make install
cpan Bio::Tools::Run::Infernal #安裝需要的perl模塊,包含cmsearch
sudo cp /usr/bin/cmsearch /usr/local/bin/
sudo cp /usr/bin/cmscan /usr/local/bin/
tRNAscan-SE -A -o 77_bin.001.tRNA.out -f 77_bin.001.rRNA.ss -m 77_bin.001.tRNA.stats 77_bin.001.fasta

eggnog (注釋)

重復(fù)序列
http://tandem.bu.edu/cgi-bin/trdb/trdb.exe?taskid=0&id=14183&accessnumber=22358
http://tandem.bu.edu/trf/trf.html

ANI-JSpecies
AAI-