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BOP phylogeny -- Click on a node to go to that page.
Node ASTRAPIAHuon astrapia314 expansions (40 rapid)455 contractions (31 rapid)135 extinctions Node LYCOCORAXSilky crow513 expansions (16 rapid)338 contractions (2 rapid)192 extinctions Node PTILORISParadise riflebird334 expansions (49 rapid)203 contractions (5 rapid)84 extinctions Node PARADISAEARed bird-of-paradise248 expansions (40 rapid)209 contractions (3 rapid)85 extinctions Node PTERIDOPHORKing of Saxony bird-of-paradise241 expansions (13 rapid)297 contractions (6 rapid)153 extinctions Node CROWHooded crow362 expansions (6 rapid)1708 contractions (45 rapid)1090 extinctions Node FICEDULAFlycatcher329 expansions (23 rapid)560 contractions (7 rapid)194 extinctions Node TAENIOPYGIAZebra finch1463 expansions (17 rapid)977 contractions (7 rapid)664 extinctions Node BOP1Concordance: NASplit time: 44.0mya16 expansions (2 rapid)71 contractions (0 rapid)0 extinctions Node BOP5Concordance: 0.26Split time: 7.59mya21 expansions (5 rapid)63 contractions (38 rapid)42 extinctions Node BOP7Concordance: 0.31Split time: 8.66mya16 expansions (4 rapid)17 contractions (5 rapid)14 extinctions Node BOP9Concordance: 0.81Split time: 10.42mya202 expansions (13 rapid)99 contractions (6 rapid)33 extinctions Node BOP11Concordance: 0.74Split time: 22.93mya356 expansions (17 rapid)246 contractions (2 rapid)95 extinctions Node BOP13Concordance: NASplit time: 37.0mya73 expansions (2 rapid)128 contractions (9 rapid)0 extinctions
|# gene families for CAFE||9010|
|CAFE estimated error||0.01025|
|CAFE estimated lambda||0.00205|
Peptides for all 8 species were obtained. All but the longest isoform of each gene was removed and an all-v-all BLAST search was performed. The e-values from the BLAST search serve as the main clustering criterion for MCL, which groups peptides into gene families. These gene families, along with the species phylogeny (obtained from ML estimation of gene trees and based on dates from Timetree.org) were given as input to CAFE to estimate gene gain and loss rates (lambda) and reconstruct ancestral gene counts..