Man pages for kullrich/MSA2dist
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis
| aa2selfscore | aa2selfscore |
| aabin2aastring | aabin2aastring |
| AAMatrix-data | AAMatrix-data |
| aastring2aabin | aastring2aabin |
| aastring2aln | aastring2aln |
| aastring2dist | aastring2dist |
| addmask2string | addmask2string |
| addpop2string | addpop2string |
| addpos2string | addpos2string |
| addregion2string | addregion2string |
| aln2aastring | aln2aastring |
| aln2dnastring | aln2dnastring |
| cds2aa | cds2aa |
| cds2codonaln | cds2codonaln |
| cdsstring2codonaln | cdsstring2codonaln |
| codon2numberAMBIG | codon2numberAMBIG |
| codon2numberTCAG | codon2numberTCAG |
| codonmat2pnps | codonmat2pnps |
| codonmat2xy | codonmat2xy |
| compareCodons | compareCodons |
| dnabin2dnastring | dnabin2dnastring |
| dnastring2aln | dnastring2aln |
| dnastring2codonmat | dnastring2codonmat |
| dnastring2dist | dnastring2dist |
| dnastring2dnabin | dnastring2dnabin |
| dnastring2kaks | dnastring2kaks |
| GENETIC_CODE_TCAG | GENETIC_CODE_TCAG |
| getmask | getmask |
| getpos | getpos |
| globalDeletion | globalDeletion |
| globalDeletionAA | globalDeletionAA |
| granthamMatrix | granthamMatrix |
| hiv-data | hiv-data |
| indices2kaks | indices2kaks |
| iupac-data | iupac-data |
| iupacMatrix | iupacMatrix |
| makePostalignedSeqs | makePostalignedSeqs |
| pal2nal | pal2nal |
| popinteger | popinteger |
| popnames | popnames |
| rcpp_distSTRING | rcpp_distSTRING |
| rcpp_KaKs | rcpp_KaKs |
| rcpp_pairwiseDeletionAA | rcpp_pairwiseDeletionAA |
| rcpp_pairwiseDeletionDNA | rcpp_pairwiseDeletionDNA |
| region | region |
| regionused | regionused |
| string2region | string2region |
| subString | subString |
| uptriidx | uptriidx |
