PHYLIP
From CLAB
PHYLIP is a free package of programs for inferring phylogenies.
Contents |
[edit] Availability
PHYLIP is 34 different programs that are simply compiled and copied into /usr/bin.
- phylogeny.ist.unomaha.edu
- klab.ist.unomaha.edu (3.68)
[edit] Usage example
Steps to create a distance matrix:
- clustalw myseqs.fasta -OUTPUT=phylip
- dnadist
- neighbor
So now you have data like this:
7 Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
fitch that bad boy.
$ cat outfile
7 Populations
Fitch-Margoliash method version 3.67
__ __ 2
\ \ (Obs - Exp)
Sum of squares = /_ /_ ------------
2
i j Obs
Negative branch lengths not allowed
+---------------------------------------------Mouse
!
! +------Human
! +--5
! +-4 +--------Chimp
! ! !
! +--3 +---------Gorilla
! ! !
1------------------------2 +-----------------Orang
! !
! +---------------------Gibbon
!
+------------------------------------------------------Bovine
remember: this is an unrooted tree!
Sum of squares = 0.01375
Average percent standard deviation = 1.85418
Between And Length
------- --- ------
1 Mouse 0.76985
1 2 0.41983
2 3 0.04986
3 4 0.02121
4 5 0.03695
5 Human 0.11449
5 Chimp 0.15471
4 Gorilla 0.15680
3 Orang 0.29209
2 Gibbon 0.35537
1 Bovine 0.91675
$ cat outtree (Mouse:0.76985,((((Human:0.11449,Chimp:0.15471):0.03695,Gorilla:0.15680) :0.02121,Orang:0.29209):0.04986,Gibbon:0.35537):0.41983,Bovine:0.91675);
drawgram outtree.
[edit] Running in batch
Click, scroll down the this section: Running the programs in background or under control of a command file
Input file can look like this:
seq.distances Y
Then you can run like this:
neighbor < input > screenout &
[edit] Installation
[edit] Installing PHYLIP itself
$ apt-cache search phylip $ apt-get install phylip
[edit] Installing the "EMBASSY" (EMBOSS) wrapper
$ apt-get install libxaw7-dev
To avoid this error: /usr/bin/ld: cannot find -lXaw
Now, you can proceed:
$ cd src $ wget ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.68.tar.gz $ tar xvzf PHYLIPNEW-3.68.tar.gz $ cd PHYLIPNEW-3.68 $ ./configure --prefix=/usr/local/share/EMBOSS $ make $ make install
-sigh- Makefile bugs? --prefix installed bin/ correctly, but everything else went to the wrong place. Fix it.
$ cd /usr/local/share/EMBOSS $ mv share/EMBOSS/acd/* acd/ $ mv share/EMBOSS/doc/html doc/ $ mv share/EMBOSS/doc/programs/text/* doc/programs/text/ $ rm -rf share/EMBOSS
[edit] Verifying Install
Create the following infile with vi or whatever:
$ cd /tmp
$ cat infile
7
Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905
Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629
Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583
Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710
Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083
Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692
Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
Then run this
$ /usr/local/share/EMBOSS/bin/ffitch infile Phylip tree file (optional): <--- leave this empty
Output file infile.ffitch should have interesting stuff in it now.
