Open Refine

http://openrefine.org/
Planilhas - merge de planilhas - importação de colunas - (...)

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Comandos comuns do PAUP - block

retirado de : http://www.peter.unmack.net/molecular/programs/paup.command.blocks.html Common PAUP analysis commands By Peter Unmack I usually paste the blocks below to the end of my nexus files, open the command line version (which runs faster than the GUI) and execute the file (I usually copy the datafile to my paup directory, or copy paup to where my datafile is).   Stuff highlighted in yellow is what usually gets changed by the user depending upon their dataset and needs. Parsimony Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgroup fish1 fish2 etc ; hsearch addseq=random nreps=1000 swap=tbr hold=1; savetrees file= datasetname .cb.pa.tree.nex format=altnex brlens=yes; pscores /tl ci ri rc; end; Parsimony Bootstrap Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgr...
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Platanus

  Platanus_trim xxx_1.fastq xxx_2.fastq   Platanus assemble -o Pxut -f ./DRR02167[34]_[12].fastq 2> assemble.log Platanus scaffold -o Pxut -c Pxut_contig.fa -b Pxut_contigBubble.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq 2> scaffold.log   Platanus gap_close -o Pxut -c Pxut_scaffold.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq 2> gapclose.log    
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