Description Usage Arguments Value Author(s) Examples
This function returns the number or positions of potentially-informative (parsimony-informative, phylogenetically-informative) sites in DNA sequence alignment.
1 |
x |
An object of class |
what |
Either of |
use.ambiguities |
Not yet available. |
Numeric (depending on what
, the number, fraction, or indices of potentially-informative nucleotide sites).
Christoph Heibl
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # example data:
# -------------
data(ips.16S)
# number of potentially-informative sites:
# ----------------------------------------
pis(ips.16S, what = "abs")
# proportion of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "frac")
# indeces of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "ind")
|
Loading required package: ape
Loading required package: colorspace
Loading required package: XML
[1] 138
[1] 36.7
[1] 3 6 13 24 45 52 59 60 68 74 85 88 89 90 91 92 101 102
[19] 103 104 105 107 108 109 111 113 117 131 133 145 147 148 149 151 168 178
[37] 181 182 183 185 186 187 188 190 191 192 193 194 195 196 197 198 199 200
[55] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
[73] 220 221 222 223 224 225 226 227 228 229 230 231 232 235 236 237 247 248
[91] 249 257 258 259 260 261 272 273 276 277 278 279 280 281 282 283 284 286
[109] 287 288 292 293 296 297 298 299 300 301 302 314 317 318 319 320 321 323
[127] 324 331 332 333 334 338 345 359 367 369 374 375
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