nm-applet -sm-disable
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Note: extractseuqence.pl : can extract seuquence according to the ID listed in a table/
     
perl /home/xiangyang/perlscript/extractseuquence.pl /home/xiangyang/Desktop/P.stutzeri_genome/Blast_A1501/filted_sequence.fasta /home/xiangyang/Desktop/P.stutzeri_genome/Blast_A1501/split/GCF_000520415.1_Pseu_aeru_BWHPSA039_V1 \ > 2222.fasta


cd /home/zilinyang/Desktop/bijiao/genoem_reorder/result/alignment2
perl /home/xiangyang/Desktop/perlscript/extractseuquence.pl ArsB_acr3_sequence.fasta Acr3_rebuild.txt \ > Acr3_rebuild.fasta
 
extractFromFasta.pl:  extract seuquence according to the multiplefasta file seuqence

perl /home/xiangyang/Desktop/perlscript/extractFromFasta.pl /home/xiangyang/goodProteins.fasta list "/home/xiangyang/Desktop/A1501list" \ > A1501.fa

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The “.htm” represents the part of the file you are renaming to “.html”, and “*.htm” tells it to find all files with that extension. For very simple renaming schemes this works just fine. If you ever need something more sophisticated, you will need to learn some scripting. http://tips.webdesign10.com/how-to-bulk-rename-files-in-linux-in-the-terminal

rename -v 's/\.fna$/\.fasta/' *.fna
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Note:contigbin   contigbinplus

perl /home/xiangyang/Desktop/perlscript/contigbin.pl 1.fasta 1.joint
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批量去掉文件名空格	
rename 's/[ ]+/_/g' *

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deletion blank row in file.txt (core_sequence.fan is your file)
perl -pi -e "s/^\n//" NC_000913.3_cds --------------------------------------------------------------------------------------------------------------------------

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Concatenate FASTA alignments to PHYML or FASTA format
USAGE

To concatenate fasta files to a phyml readable format:

    catfasta2phyml.pl file1.fas file2.fas > out.phy
    catfasta2phyml.pl *.fas > out.phy
    catfasta2phyml.pl --verbose *.fas > out.phy

To concatenate fasta files to fasta format:

perl /home/xiangyang/Desktop/perlscript/catfasta2phyml.pl -f core.xmfa.1 core.xmfa.2 > cat.fasta

perl /home/xiangyang/Desktop/perlscript/fastaConcat.pl core.xmfa.1 core.xmfa.2 > cat.fasta
catfasta2phyml.pl -f *.fas > out.fasta

To check fasta alignments

    catfasta2phyml.pl --dont-print --verbose *.fasta
    catfasta2phyml.pl -d *.fasta
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perl /home/xiangyang/perlscript/extract_header.pl
perl /home/zilinyang/Desktop/perlscript/extract_header_modified.pl
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perl /home/zilinyang/Desktop/perlscript/gbf2tbl.pl /home/zilinyang/Desktop/bijiao/covered_gbk/CP015113.gbk
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cd /home/zilinyang/Desktop/perlscript/
/home/zilinyang/Desktop/perlscript/get_cds.pl -i /home/zilinyang/Desktop/perlscript/NC_000913.3.gbk -o NC_000913.3_cds
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modified the fasta headers
cut -d " " -f 1 /home/zilinyang/Desktop/MLSA_analysis/draft.faa > delete_draft.faa