wiki:PICS-Ord

Description

PICS-Ord is an algorithm to extract phylogenetic information from hard-to-align regions of multiple sequence alignments. It has been implemented in an R-based program using Ngila as a back end.

Download

Download PICS-Ord

Installation

In order to run PICS-Ord, you need to install R on your computer. You will also need to download and install Ngila Release-1.3 or greater. After downloading the PICS-Ord package, unzip the file folder and store it on your desktop or in your preferred directory.

We recommend that you install picsord.R and picsord.bat into a folder in your path. If you are not using Windows, you do not need picsord.bat, but you will need to copy the symlink of picsord.R to picsord.

Instructions

See manual.pdf, which comes with the package.

Example Usage

picsord example1.fas > out.phy

Bugs

Empty Sequences

PICS-Ord can handle empty sequence, but due to a parsing issue in Ngila, the following input file will fail:

>Seq_1
aaaaa
>Seq_2
>Seq_3
aaaaaaaa

The parser expects "something" after the sequence name, and when you have an empty sequence, just put a space there:

>Seq_1
aaaaa
>Seq_2

>Seq_3
aaaaaaaa

R 2.12 and R 2.13

The function "cmdscale" has changed behavior in the last two major version of R. PICS-Ord has been updated to work with these versions, but should still work with older versions. Let me know if problems still persist.

Very Very Short Sequences

Using PICS-Ord on short sequences can trigger a programming bug and force the program to exit. This bug has now been fixed. (8/23/2011)

Last modified 3 years ago Last modified on Aug 23, 2011, 9:47:07 AM