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pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
GNU General Public License v3.0
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Different order of map.txt generate different results #27

Closed zhangzhiyangcs closed 2 years ago

zhangzhiyangcs commented 2 years ago

Hi, When I change the order of map.txt. Hyde generate different results below. The other data is totally same. Which results should I choose? 1) map.txt corespond to 1) hyde result. Thanks a lot.

1) map.txt

A1 PP A2 PP B1 EE B2 EE C1 TT C1 TT out Outgroup

2) map.txt

A1 PP A2 PP B1 EE B2 EE out Outgroup C1 TT C1 TT

3) map.txt

A1 PP A2 PP out Outgroup B1 EE B2 EE C1 TT C1 TT

1) hyde result

P1 Hybrid P2 Zscore Pvalue Gamma AAAA AAAB AABA AABB AABC ABAA ABAB ABAC ABBA BAAA ABBC CABC BACA BCAA ABCD PP EE TT -99999.9 1.0 -0.6460759167691903 239310514.0 4926153.0 18118082.0 5267407.0 1050209.0 2101676.0 1764620.0 117080.0 389795.0 3519108.0 109741.0 224078.0 592437.0 233609.0 35727.0 PP TT EE 314.8021752685754 0.0 0.21988626194874097 239310514.0 18118082.0 4926153.0 5267407.0 1050209.0 2101676.0 389795.0 224078.0 1764620.0 3519108.0 592437.0 117080.0 109741.0 233609.0 35727.0 EE PP TT -802.0547830469242 1.0 0.582026225720279 239310514.0 4926153.0 2101676.0 1764620.0 117080.0 18118082.0 5267407.0 1050209.0 389795.0 3519108.0 109741.0 224078.0 233609.0 592437.0 35727.0

2) hyde result

P1 Hybrid P2 Zscore Pvalue Gamma AAAA AAAB AABA AABB AABC ABAA ABAB ABAC ABBA BAAA ABBC CABC BACA BCAA ABCD PP EE TT -99999.9 1.0 -0.36171008725438364 238693380.0 5203504.0 18077744.0 5788436.0 1161575.0 1840380.0 1482371.0 102253.0 338554.0 3072035.0 105226.0 192061.0 518217.0 203247.0 32078.0 PP TT EE 289.6934294867369 0.0 0.17347121850724456 238693380.0 18077744.0 5203504.0 5788436.0 1161575.0 1840380.0 338554.0 192061.0 1482371.0 3072035.0 518217.0 102253.0 105226.0 203247.0 32078.0 EE PP TT -1090.5929335224123 1.0 0.5586215259266988 238693380.0 5203504.0 1840380.0 1482371.0 102253.0 18077744.0 5788436.0 1161575.0 338554.0 3072035.0 105226.0 192061.0 203247.0 518217.0 32078.0

3) hyde result

P1 Hybrid P2 Zscore Pvalue Gamma AAAA AAAB AABA AABB AABC ABAA ABAB ABAC ABBA BAAA ABBC CABC BACA BCAA ABCD PP EE TT 33.290576652603384 0.0 0.2156890547043237 225766655.0 4715721.0 4476232.0 2528479.0 208190.0 2942980.0 1908951.0 159003.0 2079324.0 27485012.0 1115630.0 162031.0 1032858.0 887788.0 63979.0 PP TT EE -99999.9 1.0 -0.6111334304223373 225766655.0 4476232.0 4715721.0 2528479.0 208190.0 2942980.0 2079324.0 162031.0 1908951.0 27485012.0 1032858.0 159003.0 1115630.0 887788.0 63979.0 EE PP TT -87.76407621160669 1.0 0.42028833620446854 225766655.0 4715721.0 2942980.0 1908951.0 159003.0 4476232.0 2528479.0 208190.0 2079324.0 27485012.0 1115630.0 162031.0 887788.0 1032858.0 63979.0

zhangzhiyangcs commented 2 years ago

My command "python ~/software/hybrid/HyDe/scripts/run_hyde.py -i tmp -m tmp.ID -o Outgroup -n 7 -t 10 -s 37366245".

pblischak commented 2 years ago

HyDe expects the taxa/individuals in the map to be in the same order as they are in the Phylip file with your sequence data and the results can be slightly different if not. The correct result would be the one where the map and the sequence data are in the same order

zhangzhiyangcs commented 2 years ago

After change the correct order, I get the stable results. Thanks a lot.