<?xml version="1.0" encoding="UTF-8"?>
<Application name="ClustalW" heavy="true" multyseq="true" cmd="heavy.sh clustalw clustalwaln.in $UI">
	<UserInterface>
		<Section name="General Properties" expand="true">
			<ComboBox name="Out order" cmd="/outorder=" >
				<Option name="Input" value="INPUT" selected="true"/>
				<Option name="Aligned" value="ALIGNED" selected="false"/>
			</ComboBox>
		</Section>
		<Section name="Multiple Alignments" expand="true">
			<ComboBox name="Type of sequence" cmd="/type=" >
				<Option value="Protein" selected="true"/>
				<Option value="DNA"/>
			</ComboBox>
			<ComboBox name="Protein scoring matrix" cmd="/matrix=" >
				<Option value="BLOSUM"/>
				<Option value="PAM" selected="true"/>
				<Option value="GONNET"/>
			</ComboBox>
			<ComboBox name="DNA scoring matrix" cmd="/dnamatrix=" >
				<Option value="IUB" selected="true"/>
				<Option value="CLUSTALW"/>
			</ComboBox>
			<NumberField name="Gap opening" value="10" min="0" max="100" cmd="/gapopen=" />
			<NumberField name="Gap extention" value="0.2" min="0" max="10" float="2" cmd="/gapext=" />
			<NumberField name="Gap separation" value="8" min="2" max="10" cmd="/gapdist="/>
			<CheckBox name="End gap separation" cmd="/endgaps=" yes="true" no="false" selected="true" />
			<CheckBox name="Residue-specific gaps" cmd="/nopgap=" yes="true" no="false" selected="false" />
			<CheckBox name="Hydrophilic gaps" cmd="/nohgap=" yes="gap" no="-nogap" />
			<ComboBox name="Hydrophilic residues" cmd="/hgapresidues=" >
				<Option value="A"/>
				<Option value="R"/>
				<Option value="N"/>
				<Option value="D"/>
				<Option value="C"/>
				<Option value="Q"/>
				<Option value="E"/>
				<Option value="G"/>
				<Option value="H"/>
				<Option value="I"/>
				<Option value="L"/>
				<Option value="K"/>
				<Option value="M"/>
				<Option value="F"/>
				<Option value="P"/>
				<Option value="S"/>
				<Option value="T"/>
				<Option value="W"/>
				<Option value="Y"/>
				<Option value="V"/>
			</ComboBox>
			<NumberField name="Delay divergent sequences" value="30" min="0" max="100" cmd="/maxdiv=" />
		</Section>	
		<Section name="Fast Pairwise Alignments" expand="true">
			<NumberField name="Word size" value="1" min="0" max="100" cmd="/ktuple=" />
			<NumberField name="Number of best diagonals" value="5" min="0" max="10" cmd="/topdiags=" />
			<NumberField name="Window around best diags" value="5" min="0" max="10" cmd="/window="/>
			<NumberField name="Gap penalty" value="3" min="2" max="10" cmd="/pairgap="/>
			<ComboBox name="Score" cmd="/score=" >
				<Option name="Percent" value="percent" selected="true"/>
				<Option name="Absolute" value="absolute" selected="false"/>
			</ComboBox>
		</Section>
		<Section name="Slow Pairwise Alignments" expand="true">
			<ComboBox name="Protein scoring matrix" cmd="/pwmatrix=" >
				<Option value="BLOSUM"/>
				<Option value="PAM" selected="true"/>
				<Option value="GONNET"/>
			</ComboBox>
			<ComboBox name="DNA scoring matrix" cmd="/pwdnamatrix=" >
				<Option value="IUB" selected="true"/>
				<Option value="CLUSTALW" />
			</ComboBox>
			<NumberField name="Gap opening" value="10" min="0" max="100" cmd="/pwgapopen=" />
			<NumberField name="Gap extention" value="0.2" min="0" max="10" float="2" cmd="/pwgapext=" />
		</Section>
		
		<Section name="Phylogenetic Trees" expand="true">	
			<CheckBox name="Kimura correction" yes="true" no="false" cmd="/kimura="/>
			<CheckBox name="Ignore positions with gaps" yes="true" no="false" cmd="/tossgaps="/>
			<NumberField name="Seed number for bootstraps" value="0" min="0" max="100000" cmd="/seed=" />
			<ComboBox name="Output tree" cmd="/outputtree=" >
				<Option value="phylip"/>
				<Option value="dist" selected="true"/>
				<Option value="nj"/>
			</ComboBox>
		
		
		
		</Section>
	</UserInterface>
	<Files>
		<Input>
			<File name="clustalwaln.in"/>
		</Input>
		<Output>
			<File name="clustalwaln.aln"/>
			<File name="clustalwaln.ph"/>
		</Output>
	</Files>
	<Connection>
		<Input>
			<Application name="BLASTp" file="blastp.out" file2="clustalwaln.in" filter="FastaFromBlast"/>
			<Application name="BLASTn" file="blastn.out" file2="clustalwaln.in" filter="FastaFromBlast"/>
			<Application name="tBLASTn" file="tblastn.out" file2="clustalwaln.in" filter="FastaFromBlast"/>
			<Application name="BLASTx" file="blastx.out" file2="clustalwaln.in" filter="FastaFromBlast"/>
			<Application name="tBLASTx" file="tblastx.out" file2="clustalwaln.in" filter="FastaFromBlast"/>
			<Application name="FASTa" file="fasta.out" file2="clustalwaln.in" filter="FastaFromFasta"/>
			<Application name="FASTx" file="fasta.out" file2="clustalwaln.in" filter="FastaFromFasta"/>
			<Application name="FASTy" file="fasta.out" file2="clustalwaln.in" filter="FastaFromFasta"/>
		</Input>
		<Output>
			<Application name="cons"/>
			<Application name="infoalign"/>
			<Application name="plotcon"/>
			<Application name="prettyplot"/>
			<Application name="prophecy"/>
			<Application name="distmat"/>
			<Application name="showalign"/>
		</Output>
	</Connection>
</Application>
