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test.parc
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#A NOTE ON THIS FORMAT
#The software only requires these tags :
#<CONSTRAINTS>, <GENETREE>,<SPECIESTREE>, <GENESPECIESMAPPING>,<TREEID>
#The rest is optional and is there only for the human eyes
<INSTANCE>
<NBCONSTRAINTS>
6
</NBCONSTRAINTS>
<NBBADPARALOGS>
2
</NBBADPARALOGS>
<NBGOODORTHOLOGS>
4
</NBGOODORTHOLOGS>
<NBLEAVES>
15
</NBLEAVES>
<CONSTRAINTS>
Danio rerio_ENSDARG00000075721:Homo sapiens_ENSG00000023041
Danio rerio_ENSDARG00000075721:Mus musculus_ENSMUSG00000024982
Homo sapiens_ENSG00000023041:Mus musculus_ENSMUSG00000024982
Oryzias latipes_ENSORLG00000020332:Tetraodon nigroviridis_ENSTNIG00000004699
Gasterosteus aculeatus_ENSGACG00000004937:Tetraodon nigroviridis_ENSTNIG00000004699
Danio rerio_ENSDARG00000007808:Gasterosteus aculeatus_ENSGACG00000007213
</CONSTRAINTS>
<GENETREE>
(((Danio rerio_ENSDARG00000075721, (Gasterosteus aculeatus_ENSGACG00000002103, Oryzias latipes_ENSORLG00000008423)speciation)speciation, (Homo sapiens_ENSG00000023041, Mus musculus_ENSMUSG00000024982)dubious NAD)speciation, (((Danio rerio_ENSDARG00000015989, (Oryzias latipes_ENSORLG00000020332, (Gasterosteus aculeatus_ENSGACG00000004937, Tetraodon nigroviridis_ENSTNIG00000004699)speciation)dubious NAD)speciation, (Danio rerio_ENSDARG00000007808, ((Gasterosteus aculeatus_ENSGACG00000007213, Oryzias latipes_ENSORLG00000008594)speciation, Tetraodon nigroviridis_ENSTNIG00000016520)speciation)speciation)duplication, (Mus musculus_ENSMUSG00000025157, Homo sapiens_ENSG00000171307)dubious)speciation)duplication;
</GENETREE>
<SPECIESTREE>
((((gasterosteus aculeatus, oryzias latipes), tetraodon nigroviridis), danio rerio), (mus musculus, homo sapiens));
</SPECIESTREE>
<GENESPECIESMAPPING>
Danio rerio_ENSDARG00000075721:Danio rerio
Gasterosteus aculeatus_ENSGACG00000002103:Gasterosteus aculeatus
Oryzias latipes_ENSORLG00000008423:Oryzias latipes
Homo sapiens_ENSG00000023041:Homo sapiens
Mus musculus_ENSMUSG00000024982:Mus musculus
Danio rerio_ENSDARG00000015989:Danio rerio
Oryzias latipes_ENSORLG00000020332:Oryzias latipes
Gasterosteus aculeatus_ENSGACG00000004937:Gasterosteus aculeatus
Tetraodon nigroviridis_ENSTNIG00000004699:Tetraodon nigroviridis
Danio rerio_ENSDARG00000007808:Danio rerio
Gasterosteus aculeatus_ENSGACG00000007213:Gasterosteus aculeatus
Oryzias latipes_ENSORLG00000008594:Oryzias latipes
Tetraodon nigroviridis_ENSTNIG00000016520:Tetraodon nigroviridis
Mus musculus_ENSMUSG00000025157:Mus musculus
Homo sapiens_ENSG00000171307:Homo sapiens
</GENESPECIESMAPPING>
<TREEID>
ENSGT00660000095513
</TREEID>
</INSTANCE>
<INSTANCE>
<NBCONSTRAINTS>
18
</NBCONSTRAINTS>
<NBBADPARALOGS>
9
</NBBADPARALOGS>
<NBGOODORTHOLOGS>
9
</NBGOODORTHOLOGS>
<NBLEAVES>
13
</NBLEAVES>
<CONSTRAINTS>
Danio rerio_ENSDARG00000088925:Oryzias latipes_ENSORLG00000016166
Danio rerio_ENSDARG00000088925:Gasterosteus aculeatus_ENSGACG00000011089
Danio rerio_ENSDARG00000088925:Tetraodon nigroviridis_ENSTNIG00000012461
Oryzias latipes_ENSORLG00000016166:Tetraodon nigroviridis_ENSTNIG00000012461
Gasterosteus aculeatus_ENSGACG00000011089:Tetraodon nigroviridis_ENSTNIG00000012461
Danio rerio_ENSDARG00000088925:Mus musculus_ENSMUSG00000027546
Oryzias latipes_ENSORLG00000016166:Mus musculus_ENSMUSG00000027546
Gasterosteus aculeatus_ENSGACG00000011089:Mus musculus_ENSMUSG00000027546
Tetraodon nigroviridis_ENSTNIG00000012461:Mus musculus_ENSMUSG00000027546
Danio rerio_ENSDARG00000088925:Homo sapiens_ENSG00000054793
Oryzias latipes_ENSORLG00000016166:Homo sapiens_ENSG00000054793
Gasterosteus aculeatus_ENSGACG00000011089:Homo sapiens_ENSG00000054793
Tetraodon nigroviridis_ENSTNIG00000012461:Homo sapiens_ENSG00000054793
Danio rerio_ENSDARG00000062521:Gasterosteus aculeatus_ENSGACG00000002539
Danio rerio_ENSDARG00000062521:Mus musculus_ENSMUSG00000024566
Gasterosteus aculeatus_ENSGACG00000002539:Mus musculus_ENSMUSG00000024566
Danio rerio_ENSDARG00000062521:Homo sapiens_ENSG00000166377
Gasterosteus aculeatus_ENSGACG00000002539:Homo sapiens_ENSG00000166377
</CONSTRAINTS>
<GENETREE>
(((Danio rerio_ENSDARG00000088925, (Oryzias latipes_ENSORLG00000016166, (Gasterosteus aculeatus_ENSGACG00000011089, Tetraodon nigroviridis_ENSTNIG00000012461)speciation)dubious NAD)speciation, (Mus musculus_ENSMUSG00000027546, Homo sapiens_ENSG00000054793)dubious)dubious NAD NAD NAD NAD NAD NAD NAD NAD, ((Danio rerio_ENSDARG00000062521, ((Gasterosteus aculeatus_ENSGACG00000002539, Oryzias latipes_ENSORLG00000008869)speciation, (Tetraodon nigroviridis_ENSTNIG00000002928, Tetraodon nigroviridis_ENSTNIG00000003183)duplication)speciation)speciation, (Mus musculus_ENSMUSG00000024566, Homo sapiens_ENSG00000166377)speciation)speciation)duplication;
</GENETREE>
<SPECIESTREE>
((((gasterosteus aculeatus, oryzias latipes), tetraodon nigroviridis), danio rerio), (mus musculus, homo sapiens));
</SPECIESTREE>
<GENESPECIESMAPPING>
Danio rerio_ENSDARG00000088925:Danio rerio
Oryzias latipes_ENSORLG00000016166:Oryzias latipes
Gasterosteus aculeatus_ENSGACG00000011089:Gasterosteus aculeatus
Tetraodon nigroviridis_ENSTNIG00000012461:Tetraodon nigroviridis
Mus musculus_ENSMUSG00000027546:Mus musculus
Homo sapiens_ENSG00000054793:Homo sapiens
Danio rerio_ENSDARG00000062521:Danio rerio
Gasterosteus aculeatus_ENSGACG00000002539:Gasterosteus aculeatus
Oryzias latipes_ENSORLG00000008869:Oryzias latipes
Tetraodon nigroviridis_ENSTNIG00000002928:Tetraodon nigroviridis
Tetraodon nigroviridis_ENSTNIG00000003183:Tetraodon nigroviridis
Mus musculus_ENSMUSG00000024566:Mus musculus
Homo sapiens_ENSG00000166377:Homo sapiens
</GENESPECIESMAPPING>
<TREEID>
ENSGT00550000074723
</TREEID>
</INSTANCE>
<INSTANCE>
<NBCONSTRAINTS>
1
</NBCONSTRAINTS>
<NBBADPARALOGS>
1
</NBBADPARALOGS>
<NBGOODORTHOLOGS>
0
</NBGOODORTHOLOGS>
<NBLEAVES>
11
</NBLEAVES>
<CONSTRAINTS>
Gasterosteus aculeatus_ENSGACG00000007592:Oryzias latipes_ENSORLG00000017756
</CONSTRAINTS>
<GENETREE>
(((Danio rerio_ENSDARG00000076768, (Tetraodon nigroviridis_ENSTNIG00000005471, Oryzias latipes_ENSORLG00000016343)speciation)speciation, (Homo sapiens_ENSG00000169891, Mus musculus_ENSMUSG00000040855)speciation)speciation, ((Danio rerio_ENSDARG00000002877, ((Gasterosteus aculeatus_ENSGACG00000007592, Tetraodon nigroviridis_ENSTNIG00000012206)speciation, Oryzias latipes_ENSORLG00000017756)dubious NAD)speciation, (Mus musculus_ENSMUSG00000019854, Homo sapiens_ENSG00000135597)dubious)speciation)duplication;
</GENETREE>
<SPECIESTREE>
((((gasterosteus aculeatus, oryzias latipes), tetraodon nigroviridis), danio rerio), (mus musculus, homo sapiens));
</SPECIESTREE>
<GENESPECIESMAPPING>
Danio rerio_ENSDARG00000076768:Danio rerio
Tetraodon nigroviridis_ENSTNIG00000005471:Tetraodon nigroviridis
Oryzias latipes_ENSORLG00000016343:Oryzias latipes
Homo sapiens_ENSG00000169891:Homo sapiens
Mus musculus_ENSMUSG00000040855:Mus musculus
Danio rerio_ENSDARG00000002877:Danio rerio
Gasterosteus aculeatus_ENSGACG00000007592:Gasterosteus aculeatus
Tetraodon nigroviridis_ENSTNIG00000012206:Tetraodon nigroviridis
Oryzias latipes_ENSORLG00000017756:Oryzias latipes
Mus musculus_ENSMUSG00000019854:Mus musculus
Homo sapiens_ENSG00000135597:Homo sapiens
</GENESPECIESMAPPING>
<TREEID>
ENSGT00530000063792
</TREEID>
</INSTANCE>