codoncode aligner blast search not working

#CODONCODE ALIGNER BLAST SEARCH NOT WORKING FULL#

trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. ML trees showed the highest mean support value (80.95%).

#CODONCODE ALIGNER BLAST SEARCH NOT WORKING FULL#

Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). rbcLa showed the highest species discrimination in BLASTn (66.67%). Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.ĭNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. Species discrimination did not increase using rbcLa + trnH-psbA. trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e-16). DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants.

Codoncode aligner blast search not working