MSA2dist calculates pairwise distances for
DNAStringSet/AAStringSet using custom scoring, conducts codon
analyses (including dNdS), and estimates Dxy/FST
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Documentation for package ‘MSA2dist’ version 1.17.8
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| aa2selfscore | aa2selfscore |
| aabin2aastring | aabin2aastring |
| AAMatrix | AAMatrix-data |
| 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 |
| codon2number | GENETIC_CODE_TCAG |
| codon2numberAMBIG | codon2numberAMBIG |
| codon2numberTCAG | codon2numberTCAG |
| codonmat2pnps | codonmat2pnps |
| codonmat2xy | codonmat2xy |
| collapseChar | collapseChar |
| collapseXStringSet | collapseXStringSet |
| compareCodons | compareCodons |
| dist2dxy | dist2dxy |
| dnabin2dnastring | dnabin2dnastring |
| dnastring2aln | dnastring2aln |
| dnastring2codonmat | dnastring2codonmat |
| dnastring2dist | dnastring2dist |
| dnastring2dnabin | dnastring2dnabin |
| dnastring2dxy | dnastring2dxy |
| dnastring2kaks | dnastring2kaks |
| dnastring2weightedPi | dnastring2weightedPi |
| GENETIC_CODE_TCAG | GENETIC_CODE_TCAG |
| getmask | getmask |
| getpos | getpos |
| globalDeletion | globalDeletion |
| globalDeletionAA | globalDeletionAA |
| granthamMatrix | granthamMatrix |
| hiv | hiv-data |
| hiv-data | hiv-data |
| indices2kaks | indices2kaks |
| iupac | iupac-data |
| iupac-data | iupac-data |
| iupacMatrix | iupacMatrix |
| makePostalignedSeqs | makePostalignedSeqs |
| normpop | normpop |
| pal2nal | pal2nal |
| popinteger | popinteger |
| popnames | popnames |
| rcpp_distSTRING | rcpp_distSTRING |
| rcpp_dxy_fst_pop | rcpp_dxy_fst_pop |
| rcpp_KaKs | rcpp_KaKs |
| rcpp_pairwiseDeletionAA | rcpp_pairwiseDeletionAA |
| rcpp_pairwiseDeletionDNA | rcpp_pairwiseDeletionDNA |
| rcpp_weightedPi | rcpp_weightedPi |
| rcpp_weightedPi_pop | rcpp_weightedPi_pop |
| region | region |
| regionused | regionused |
| string2region | string2region |
| subString | subString |
| uptriidx | uptriidx |