<?xml version="1.0" encoding="UTF-8"?>
<!--WARNING: Do not change anything inside this workflow file. BioExtract won't recognize your changes, or may even refuse to import it. Instead, modify the workflow in BioExtract after importing. This workflow file can be imported into BioExtract only.-->
  <s:bioextract xmlns:s="http://bioextract.org" version="2.1" log="0">
<s:workflowdescription description="This workflow provides a simple phylogenic analysis starting from a protein query using ?MrBayes? program and according to the maximum likelihood model" author="yosr.bouhlal@gmail.com" uid="1270f87c-d5ce-470c-87fa-a42e8e630d8f" title="Phylogenetic analysis workflow"/>
<s:processor name="query"><s:stringconstant>NCBI:protein:NP_000135</s:stringconstant></s:processor><s:processor name="blastp"><s:description>"Search a protein database using a protein query"</s:description><s:helpurl>"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs"</s:helpurl><s:parameter name="Select database" value="nr"/><s:parameter name="Do CD-Search" value="checkbox-on"/><s:parameter name="Limit to the organism" value="All organisms"/><s:parameter name="Expect" value="10"/><s:parameter name="Word size" value="w_3"/><s:parameter name="Matrix" value="BLOSUM62"/><s:parameter name="Gap costs" value="Existence_11_Extension_1"/><s:parameter name="Filter: Low-complexity" value="checkbox-on"/><s:parameter name="Filter: Human repeats" value="checkbox-on"/><s:parameter name="Filter: Mask for lookup table only" value="checkbox-on"/><s:parameter name="Show graphical overview" value="checkbox-on"/><s:parameter name="Show database linkouts" value="checkbox-on"/><s:parameter name="Number of descriptions" value="d_100"/><s:parameter name="Number of alignments" value="a_100"/><s:parameter name="maximum number of sequences" value="100"/></s:processor><s:processor name="xmknr"><s:description>"Reads multiple sequence records in FASTA format and removes duplicates"</s:description><s:helpurl>"http://www.vmatch.de/"</s:helpurl><s:parameter name="Sequence type (protein or DNA)" value="protein"/><s:parameter name="Minimum sequence length to include" value="1"/><s:parameter name="xdrop value for edit distance" value="2"/><s:parameter name="Small cluster value" value="90"/><s:parameter name="Large cluster value" value="90"/></s:processor><s:processor name="ClustalW2"><s:description>"Multiple Sequence Alignments"</s:description><s:helpurl>"http://www.clustal.org/download/clustalw_help.txt"</s:helpurl><s:parameter name="Output format" value="clustal"/><s:parameter name="Sequence type" value="protein"/><s:parameter name="Pairwise alignment" value="fast"/><s:parameter name="Scoring method" value="percent"/><s:parameter name="Select weight matrix" value="blosum"/></s:processor><s:processor name="make_mb_nex"><s:description>"Converts an aln file to nexus format with a mrbayes block"</s:description><s:helpurl>"http://bioservices.usd.edu/bioextract/help/make_mb_nex.html"</s:helpurl><s:parameter name="nst" value="6"/><s:parameter name="rates" value="Equal"/><s:parameter name="ngen" value="1000"/><s:parameter name="samplefreq" value="10"/><s:parameter name="Burnin for Sump" value="25"/><s:parameter name="Burnin for Sumt" value="25"/><s:parameter name="Output file name" value="mrbayes-input.nex"/><s:parameter name="Process protein input (default: dna)" value="checkbox-on"/></s:processor><s:processor name="MrBayes"><s:description>"MrBayes is a program for the Bayesian estimation of phylogeny"</s:description><s:helpurl>"http://mrbayes.csit.fsu.edu"</s:helpurl></s:processor><s:link source="query:value" sink="blastp:sequence_usa" />
<s:link source="blastp:outseq" sink="xmknr:sequences_direct_data" />
 <s:link source="xmknr:Graphics_in_PNG" sink="xmknr" />
<s:sink name="xmknr">
 <s:metadata> <s:mimeTypes>
<s:mimeType>image/png</s:mimeType>
 </s:mimeTypes> </s:metadata> </s:sink>
  </s:bioextract>