Description Usage Arguments Details Value See Also Examples
Given a set of DNA sequence alignments, raxml.partitions
creates a data frame with partition bounderies that can be input into raxml
.
1 |
... |
Two or more DNA sequence alignments of class |
For raxml.partitions
to make sense, the DNA sequence alignments must be given exactly in the same order in which they are concatenated into a supermatrix (see Examples section). Without any testing, the type of sequences is supposed to be DNA.
A data frame with four columns (type
, locus
, begin
, and end
) and number of rows corresponding to the number of partitions.
cbind.DNAbin
to concatenate multiple alignments; raxml
for an interface to RAxML.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
Loading required package: ape
Loading required package: colorspace
Loading required package: XML
type locus begin end
1 DNA cox1 1 770
2 DNA r16S 771 1146
3 DNA r28S 1147 1708
48 DNA sequences in binary format stored in a matrix.
All sequences of same length: 1708
Labels:
Ips_avulsus
Ips_confusus
Ips_cribricollis
Ips_borealis
Ips_pilifrons
Ips_nitidus
...
Base composition:
a c g t
0.304 0.168 0.190 0.338
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