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<lamarc-converter-cmd>
<lamarc-header-comment>traitExample: generated with theta=0.1 rec=0.1 trait at position 906</lamarc-header-comment>
<outfile>lamarc-trait-input.xml</outfile>
<traits>
<trait-info>
<name>funny-nose</name>
<allele>normal</allele>
<allele>affected</allele>
</trait-info>
<phenotype>
<name>straight</name>
<genotype-resolutions>
<trait-name>funny-nose</trait-name>
<haplotypes>
<alleles> normal normal </alleles>
<penetrance> 1.0 </penetrance>
</haplotypes>
</genotype-resolutions>
</phenotype>
<phenotype>
<name>bent</name>
<genotype-resolutions>
<trait-name>funny-nose</trait-name>
<haplotypes>
<alleles> normal affected </alleles>
<penetrance> 1.0 </penetrance>
</haplotypes>
<haplotypes>
<alleles> affected normal </alleles>
<penetrance> 1.0 </penetrance>
</haplotypes>
</genotype-resolutions>
</phenotype>
<phenotype>
<name>broken</name>
<genotype-resolutions>
<trait-name>funny-nose</trait-name>
<haplotypes>
<alleles> affected affected </alleles>
<penetrance> 1.0 </penetrance>
</haplotypes>
</genotype-resolutions>
</phenotype>
</traits>
<regions>
<region>
<name>region1</name>
<effective-popsize>1</effective-popsize>
<trait-location>
<trait-name>funny-nose</trait-name>
</trait-location>
<segments>
<segment datatype="dna">
<name>locus_1</name>
<markers>1000</markers>
<first-position-scanned>1</first-position-scanned>
<map-position>1</map-position>
</segment>
</segments>
</region>
</regions>
<populations>
<population>pop1</population>
</populations>
<individuals>
<individual>
<name>s0_s1</name>
<sample><name>s0</name></sample>
<sample><name>s1</name></sample>
<has-phenotype>broken</has-phenotype>
</individual>
<individual>
<name>s2_s3</name>
<sample><name>s2</name></sample>
<sample><name>s3</name></sample>
<has-phenotype>broken</has-phenotype>
</individual>
<individual>
<name>s4_s5</name>
<sample><name>s4</name></sample>
<sample><name>s5</name></sample>
<has-phenotype>broken</has-phenotype>
</individual>
<individual>
<name>s6_s7</name>
<sample><name>s6</name></sample>
<sample><name>s7</name></sample>
<has-phenotype>bent</has-phenotype>
</individual>
<individual>
<name>s10_s11</name>
<sample><name>s10</name></sample>
<sample><name>s11</name></sample>
<has-phenotype>straight</has-phenotype>
</individual>
<individual>
<name>s12_s13</name>
<sample><name>s12</name></sample>
<sample><name>s13</name></sample>
<has-phenotype>straight</has-phenotype>
</individual>
<individual>
<name>s14_s15</name>
<sample><name>s14</name></sample>
<sample><name>s15</name></sample>
<has-phenotype>straight</has-phenotype>
</individual>
<individual>
<name>s8_s9</name>
<sample><name>s8</name></sample>
<sample><name>s9</name></sample>
<has-phenotype>straight</has-phenotype>
</individual>
</individuals>
<infiles>
<infile format="migrate" datatype="dna" sequence-alignment="sequential">
<name>traitData.mig</name>
<population-matching type="single">pop1</population-matching>
<segments-matching type="single">locus_1</segments-matching>
</infile>
</infiles>
</lamarc-converter-cmd>
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