File: exported-lamarc-input.html

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lamarc 2.1.10.1%2Bdfsg-3
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<HTML>
<BODY>
<pre>
&lt?xml version="1.0" ?&gt
&lt!--Example output for 3 chromosomes, some with multiple segments--&gt
&ltlamarc version="2.1"&gt
    &ltformat&gt
        &ltconvert-output-to-eliminate-zero&gttrue&lt/convert-output-to-eliminate-zero&gt
    &lt/format&gt
    &ltdata&gt
        &ltregion name="chrom1"&gt
            &lteffective-popsize&gt1.000000&lt/effective-popsize&gt
            &ltspacing&gt
                &ltblock name="chrom1-segment" /&gt
            &lt/spacing&gt
            &ltpopulation name="North"&gt
                &ltindividual name="n_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind0_a"&gt
                        &ltdatablock type="DNA"&gt ccccccAcc &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind0_b"&gt
                        &ltdatablock type="DNA"&gt TcccccAcc &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind1_a"&gt
                        &ltdatablock type="DNA"&gt ccccccTcc &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind1_b"&gt
                        &ltdatablock type="DNA"&gt TcccccTcc &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind2"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind2_a"&gt
                        &ltdatablock type="DNA"&gt ccccccGcc &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind2_b"&gt
                        &ltdatablock type="DNA"&gt TcccccGcc &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
            &ltpopulation name="South"&gt
                &ltindividual name="s_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind0_a"&gt
                        &ltdatablock type="DNA"&gt cTccTcccc &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind0_b"&gt
                        &ltdatablock type="DNA"&gt ccccTcccc &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="s_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind1_a"&gt
                        &ltdatablock type="DNA"&gt cTccccccc &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind1_b"&gt
                        &ltdatablock type="DNA"&gt ccccccccc &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
        &lt/region&gt
        &ltregion name="chrom2"&gt
            &lteffective-popsize&gt1.000000&lt/effective-popsize&gt
            &ltspacing&gt
                &ltblock name="chrom2-segment1"&gt
                    &ltmap-position&gt 1000 &lt/map-position&gt
                    &ltlength&gt 500 &lt/length&gt
                    &ltoffset&gt -4 &lt/offset&gt
                    &ltlocations&gt 2 88 125 173 443 &lt/locations&gt
                &lt/block&gt
                &ltblock name="chrom2-segment2"&gt
                    &ltmap-position&gt 5000 &lt/map-position&gt
                    &ltlength&gt 250 &lt/length&gt
                    &ltoffset&gt -4 &lt/offset&gt
                    &ltlocations&gt 13 19 35 77 102 112 204 &lt/locations&gt
                &lt/block&gt
            &lt/spacing&gt
            &ltpopulation name="North"&gt
                &ltindividual name="n_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt13 19&lt/phase&gt
                    &ltsample name="n_ind0_a"&gt
                        &ltdatablock type="SNP"&gt Gaaaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt Caaaaaa &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind0_b"&gt
                        &ltdatablock type="SNP"&gt aGaaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aCaaaaa &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind1_a"&gt
                        &ltdatablock type="SNP"&gt aaGaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaCaaaa &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind1_b"&gt
                        &ltdatablock type="SNP"&gt aaaGa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaaCaaa &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind2"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind2_a"&gt
                        &ltdatablock type="SNP"&gt aaaaG &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaaaCaa &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind2_b"&gt
                        &ltdatablock type="SNP"&gt Taaaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaaaaCa &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
            &ltpopulation name="South"&gt
                &ltindividual name="s_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind0_a"&gt
                        &ltdatablock type="SNP"&gt Taaaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt Gaaaaaa &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind0_b"&gt
                        &ltdatablock type="SNP"&gt aTaaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aGaaaaa &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="s_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind1_a"&gt
                        &ltdatablock type="SNP"&gt aaTaa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaGaaaa &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind1_b"&gt
                        &ltdatablock type="SNP"&gt aaaTa &lt/datablock&gt
                        &ltdatablock type="SNP"&gt aaaGaaa &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
        &lt/region&gt
        &ltregion name="chrom3"&gt
            &ltspacing&gt
                &ltblock name="chrom3-micro"&gt
                    &ltmap-position&gt 500 &lt/map-position&gt
                    &ltoffset&gt 1 &lt/offset&gt
                &lt/block&gt
                &ltblock name="chrom3-snp"&gt
                    &ltmap-position&gt 501 &lt/map-position&gt
                    &ltlength&gt 100 &lt/length&gt
                    &ltoffset&gt 1 &lt/offset&gt
                    &ltlocations&gt 23 &lt/locations&gt
                &lt/block&gt
            &lt/spacing&gt
            &ltpopulation name="North"&gt
                &ltindividual name="n_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind0_a"&gt
                        &ltdatablock type="Microsat"&gt  18 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt T &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind0_b"&gt
                        &ltdatablock type="Microsat"&gt  18 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind1_a"&gt
                        &ltdatablock type="Microsat"&gt  18 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind1_b"&gt
                        &ltdatablock type="Microsat"&gt  19 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="n_ind2"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="n_ind2_a"&gt
                        &ltdatablock type="Microsat"&gt  18 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt A &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="n_ind2_b"&gt
                        &ltdatablock type="Microsat"&gt  20 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
            &ltpopulation name="South"&gt
                &ltindividual name="s_ind0"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind0_a"&gt
                        &ltdatablock type="Microsat"&gt  19 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt G &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind0_b"&gt
                        &ltdatablock type="Microsat"&gt  20 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
                &ltindividual name="s_ind1"&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltphase type="unknown"&gt&lt/phase&gt
                    &ltsample name="s_ind1_a"&gt
                        &ltdatablock type="Microsat"&gt  19 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                    &ltsample name="s_ind1_b"&gt
                        &ltdatablock type="Microsat"&gt  21 &lt/datablock&gt
                        &ltdatablock type="SNP"&gt c &lt/datablock&gt
                    &lt/sample&gt
                &lt/individual&gt
            &lt/population&gt
        &lt/region&gt
    &lt/data&gt
&lt/lamarc&gt
</pre>
</BODY>
</HTML>