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veg / hyphy

HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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one codon sequence can not be detected when it was inputted together with other 28 sequences #1015

Closed ybdong919 closed 5 years ago

ybdong919 commented 5 years ago

one codon sequence can not be detected when it was inputted together with other 28 sequences. The sequence is :

QY6AD9.2

------------------------ATGGGGAGCAAGGATAGAATATCATTGCACCCGCCA TATGTGAGGGGTTCTCCCCCTTCAGGTCCTGGT---TTGTTGCATTCTGAGCCA------ CTCACTATGCAC------------CATCCGCCTGTTCGGCATGCGCCATATGATATGTTG CCACACTCCGAAGTTATGGAGCGGAGGCTTGCTGACCAGCAGCTGCAGATGCAGAGGTTA GACTATGGAAACCGGAGGCTCTCTGACCAGCACACGGAGATGCAAAGGCTGGACTATGAA AACCAAAGGCTTGCAGCTTCCCATGGGACATTGAGGCAGGAGCTCATTGCAGCACAGCGT GAACTGCAAGTGTTGCAATCGCAAATTGGCACTGCAGAGGCCAAGAGGGAGCAGCAGATT CGGGGTGTCGTAGATGAAATTGCTAGGATGGAGGCTGAGCTGCAGGCTGCAGAGCCTCTC AAGCATGAACTGCAACGAGCGCAGGGTGAGGCTCAGAGCCTGGTTGTTTCTAGGGAGGAG CTTGTTTCTAATGCGCAGAAGCTGTCTCAAGAACTTCAGAGAACCTTCGCAGATGTGCAG CAGATTCCAGCTCTGATGTCGGAATTTGAGGGCCTCAGACAA---------GAATATCAG

------------------------------------------------------CATTGC AGGGCCACTTTTGAATGTGAAAAAAAATTATACAATGACCATCTTAAGTCACTTCAAGAG ATGGAAAATAACTATGCTTCTATGTCTAAAGAAGTGGAAAAACTCCGAGCAGAGCTTACG AACACTGTTAATGTTAATCAAAGA------AGTAGTGGTTCTTACGGAGGCTCCTCTACT ACTATGGACAATGAGGCTTATGGCCTTTCTAAGAGACAAAATGCACATGAAGATGGTTAT GTTGTTTCCCAGGGATATGGTACCCTCCTCACAGCCAGT---------------------

---GTTGGTGGCACTACTGCAACTACTACTGGAGCTCAACCTGGTCCGGCTTCTGCAAAC AATGGGTTTAATGCTCCCAGCTGG------------------------------------ ------------------------------------TCAAATTATGATTCATCTGCTGGT CCTGCTTATGATCCACAGAGGTCTGTTGCTTACGATGCACAGAGGGTGACTGGTGTTGAT TCGGTTACACAA---TCTGGCTATGATTCACAGAGAGAAGCAAATTTGAATGCT------ ------CAATATGATCCACATAGAGGT---ACAGGTTATGGCATGCAGGGAGGTCCAGGT TATGATGCC------------AGTCGAGACCAAGGTTATGATATGCAGAGACGGCCTGCT TATAATGCATCC---GGAGCTATTGGCTATGAACCGCAGTCAATAGCTGCTGGTGGTCCT CATGGACATGCTCTGCCAGTGGAGACT------ATGCTGCCTTATGGATCTACAACACCG CCGGCTCATAATAGT------GGTGGATATGAGAATTTGCATCAAGCGGTAAACCGA---

I don't know the reason why this sequence can no be found when I input all aligned sequences into Datamonkey website.

spond commented 5 years ago

Please provide the entire alignment file. There is insufficient information in your post to determine what went wrong.

Best, Sergei

ybdong919 commented 5 years ago

29CDS_codon_align.txt

spond commented 5 years ago

Dear @ybdong919,

You have 2 identical sequences in your alignment. Datamonkey will strip identical sequences out because they don't contribute any signal to selection analyses other than to make them run a bit slower.

Best. Sergei

ybdong919 commented 5 years ago

No, they are all different. Please see below all names,

Aduranensis|XP_015946425.1 Aduranensis|XP_015962559.1 Ahypogaea|5590XE.1 |   Ahypogaea|KBYC2D.1 |   Ahypogaea|QY6AD9.2 |   Ahypogaea|VC1ZWY.1 |   Aipaensis|XP_016181508.1 |   Aipaensis|XP_016194491.1 |   Athaliana|AT1G67170.1 |   Carietinum|Ca_06001.1 |   Ccajan|KYP76498.1 |   |   Gmax|18G279600.1.p |   Gsoja|KHN13801.1 |   |   Gsoja|KHN14477.1 |   |   Langustifolius|Lup001626.1 |   Langustifolius|Lup026705.2 |   Langustifolius|Lup032436.1 |   Ljaponicus|Lj1g3v3105130.2 |   Msativa|MSAD_269180.t1 |   Msativa|MSAD_314545.t1 |   Mtruncatula|Medtr7g019180.1 Ptrichocarpa|017G109700.1.p |   Pvulgaris|008G021400.1.p |   Tsubterraneum|GAU14086.1 |   Tsubterraneum|GAU14087.1 |   Vangularis|vigan.Vang04g02460.1 Vradiata|Vradi04g09970.1 |   Vunguiculata|Vigun01g238700.1.p Vunguiculata|Vigun05g023000.1.p

spond commented 5 years ago

Dear @ybdong919,

The names don't matter. The sequences themselves are not all different.

Best, Sergei

ybdong919 commented 5 years ago

Aipaensis|XP_016181508.1 and Ahypogaea|QY6AD9.2 are two genes in different species, although their sequences are same. So is there any method or setting to keep both of them?

ybdong919 commented 5 years ago

Thanks, I think you are right. keeping one seq is OK. Thanks again!