I've been continuing to plug away at Rphylip, our new R interface for Joe Felsenstein's phylogeny methods package PHYLIP. More information about this effort can be found here: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. The latest additions are Rkitsch, an interface for KITSCH (a least-squares & ME inference program with a clock constraint); Rrestdist, an interface for RESTDIST (a program for distance calculation from restriction site or fragment data); Rrestml, an interface for RESTML (a restriction site ML tree inference program); and Rclique, an interface for CLIQUE (phylogeny inference from binary characters by the compatibility method). I also added a new object class, "rest.data", for restriction data, as well as some methods to convert to the class & print.
Rphylip is on GitHub, and the latest build can be downloaded & installed from source.
Here's a quick demo of Rrestml using the demo dataset from the RESTML documentation in PHYLIP:
Loading required package: Rphylip
Loading required package: ape
> packageVersion("Rphylip")
[1] ‘0.1.20’
> data(restriction.data)
> restriction.data
13 restriction site scores for 5 species stored in a object of class "rest.data".
All sequences of same length: 13
Number of restriction enzymes used to generate the data: 2
Labels: Alpha Beta Gamma Delta Epsilon
> mltree<-Rrestml(restriction.data,quiet=TRUE)
Restriction site Maximum Likelihood method, version 3.695
Recognition sequences all 6 bases long
Sites absent from all species are assumed to have been omitted
+2
+--1
| | +4
| +--2
| +5
|
3----3
|
+1
remember: this is an unrooted tree!
Ln Likelihood = -40.31850
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
3 1 0.01396 ( zero, 0.04907)
1 2 0.00064 ( zero, infinity)
1 2 0.05872 ( zero, 0.12666) **
2 4 0.01447 ( zero, 0.04458) **
2 5 0.00100 ( zero, infinity)
3 3 0.10801 ( 0.01151, 0.21877) **
3 1 0.01046 ( zero, 0.04404)
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
> plot(mltree,no.margin=TRUE,type="unrooted",edge.width=2)
OK. That's all for now. We're still working on documentation & examples, but hopefully we will have a version on CRAN before too long.
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