It's that time of year again!! Just when you've finished ripping your hair out instailling BioPerl on Mavericks, Mac decides that it is not pissing off its users enough and decides to upgrade its operating system. And just when you can't take the notifications any longer, you are faced with that critical decision: jeapardize the security of your system for the sake of never having to reinstall bioperl, or update the OSX and know that the impending doom of reinstalling bioperl lingers--waiting to ruin your afternoon.

Well, it did just that! After hundreds of attempts to try to find the missing YAML library, I had to resort to installing perlbrew, which I did once, and it didn't work for me, but then I tried a different aspect of implementing the implementation in perlbrew several hours later, and it happened to work. If you are having serious trouble from the suggested cpan installation, give this a try:

curl -L http://install.perlbrew.pl | bash

source ~/perl5/perlbrew/etc/bashrc #and put this in your .bash_profile

#now we are going to pretend like we are in cpan, but we have to give ourselves permission first

#change your user name from mine (in pink)

sudo chown loloyohe /Users/loloyohe/.cpanm

#install cpanm

perlbrew install-cpanm

#install the builder from CPAN--oh, NOW it knows where YAML is!!!! >:|

sudo cpanm install Module::Build

#nothing really prints to screen, but it works!
#visit https://www.cpan.org/authors/id/C/CJ/CJFIELDS/ to get the latest version

sudo cpanm install CJFIELDS/BioPerl-1.6.923.tar.gz

#test to see if it works!

perl -MBio::Seq -e 0

Naturally, you will likely not have any of the same issues as me but a completely unique set of horrific issues specific to you! 

I am using modelOmatic to determine which models best fit the sequences, and it include comparisons of codon models. Installing and running modelOmatic. For awhile I thought I was having Yosemite issues but because they are all binaries, everything seems to checking out okay. Lots of "duh" moments were had.

To install on Mac OSX Yosemite:
[1] Download the binaries and move to where you store your programs.

mv ~/Downloads/modelomatic_OSX /usr/local/bin/

[2] Set modelOmatic into your path.

vi .bash_profile  #in your home directory, this opens up your bash profile

#press "i" to edit and then paste this into your .bash_profile

export PATH=/usr/local/bin/modelomatic_OSX:$PATH 

#press ESC, then type "wq!"; restart the terminal

[3] ModelOmatic requires a tree file to run. It can make a NJ tree if you have bioNJ set up. Download the binaries for bioNJ here.

[4] Move the bioNJ into where you store your programs. Set your path. You have to rename your path in lower case so that modelOmatic can read it.

mv ~/Downloads/BIONJ/ /usr/local/bin/ 

mv /usr/local/bin/BIONJ/BIONJ /usr/local/bin/BIONJ/bionj

#add to your path variable
vi .bash_profile

export PATH=/usr/local/bin/BIONJ/BIONJ:$PATH

export PATH=/usr/local/bin/BIONJ:$PATH

The format for input 

./ModelOMatic <data> bionj <output> <genetic_code> fast

I am running it as modelomatic_OSX because it is in my path. 

Using the bionj option tell modelOmatic to make its own tree using bioNJ.

Specify in <output> slot where to put your output folder.

The <genetic_code> has been tricky. It can choke and tell you that you have stop codons if you don't use the correct number:

     0:  Universal code
     1:  Vertebrate mt
     2:  Yeast mt
     3:  Mould mt

     4:  Invertebrate mt
     5:  Ciliate nuclear
     6:  Echinoderm mt
     7:  Euplotid mt

     8:  Alternative yeast nuclear
     9:  Ascidian mt

     10: Blepharisma nuclear

     11: Everything codes (64 character state-space)

My adviser was having trouble but then realized she was using cytb so it actually should have been "1" instead of "0". 

ModelOmatic uses .phylip file. Allegedly can use other formats but I have not tried. However, it actually seems ridiculously flexible in reading a .phylip file.

OR_alignments loloyohe$ modelomatic_OSX Phyllos_OR6_Funct_tAlign.phylip bionj test.txt 1

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: <Phyllos_OR6_Funct_tAlign.phylip>: 35 sequences of length 729 (DataMatrix: 35 x 570)

Checking for sparse (>85% gaps) sequences

Starting with 35 ... after removal there are 35 sequences

Creating start tree ... 

Assertion failed: (0), function Error, file tools.cxx, line 235.

Unrecognised codon: AGA for data codon position 241 in sequence 1...Abort trap: 6

We had stop codons. Okay, so I translated the sequences, looked for where the stop codons were, and then I replaced them in the original .phylip file using "---".  Note in the future that all .phylip sequence files in /Volumes/Yango/Hayden_ORs/OR_alignments have the stop codon replaced, while the .nex files have the original sequence alignments. Lets try to get it running...

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR4_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR4_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR4_Funct_tAlign.phylip>: 127 sequences of length 753 (DataMatrix: 127 x 666)

Checking for sparse (>85% gaps) sequences

Starting with 127 ... after removal there are 127 sequences

Creating start tree ...  estimated using bionj (1.15646s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (3.56514s)

NT Done  (10.6517s)

AA Done  (71.2184s).........

Codon Done  (232.733s)

Outputting results to <Phyllos_OR4_Funct_tAlign_mOm_results.txt>

Successful exit

####now for the others

modelomatic_OSX /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR6_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR6_Funct_tAlign_mOm_results.txt 0 fast

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR10_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR10_Funct_tAlign_mOm_results.txt 0 fast

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR51_Funct_tAlign_mOm_results.txt 0 fast

Had a hiccup with this data:

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR2_13_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR2_13_Funct_tAlign_mOm_results.txt 0 normal

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR2_13_Funct_tAlign.phylip>: 264 sequences of length 1530 (DataMatrix: 264 x 943)

Checking for sparse (>85% gaps) sequences

Starting with 264 ... after removal there are 264 sequences

Creating start tree ...  estimated using bionj (4.68751s)

Optimisation settings: normal 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

Broken Prob(): -0.000104812

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR137_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR137_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR137_Funct_tAlign.phylip>: 452 sequences of length 804 (DataMatrix: 452 x 766)

Checking for sparse (>85% gaps) sequences

Starting with 452 ... after removal there are 452 sequences

Creating start tree ...  estimated using bionj (4.7425s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (8.05337s)

NT Done  (44.7082s)

Broken Prob(): -40.8111

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR52_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/Phyllos_OR52_Funct_tAlign_mOm_results.txt 0 fast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip>: 152 sequences of length 750 (DataMatrix: 152 x 712)

Checking for sparse (>85% gaps) sequences

Starting with 152 ... after removal there are 152 sequences

Creating start tree ...  estimated using bionj (1.32059s)

Optimisation settings: fast 

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (4.69988s)

NT Done  (13.8241s)

AA Done  (85.6409s).........

...

Broken Prob(): -2.64535e+41

I think the problem is in running the "fast" option with large datasets. When I use "trimfast" and "normal", they both work. 

modelomatic_OSX  /Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip bionj /Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt 0 trimfast

---------------------------------------------------------------------------------------------

  ModelOMatic (v1.01 (release)).

A program for choosing substitutions models for phylogenetic inference.

Written by Simon Whelan.

Contributions from James Allen, Ben Blackburne and David Talavera.

---------------------------------------------------------------------------------------------

Data: </Volumes/Yango/Hayden_batORs/OR_alignments/Phyllos_OR51_Funct_tAlign.phylip>: 152 sequences of length 750 (DataMatrix: 152 x 712)

Checking for sparse (>85% gaps) sequences

Starting with 152 ... after removal there are 152 sequences

Creating start tree ...  estimated using bionj (1.58694s)

Optimisation settings: fast trim=10

TRIMMING: Tree contains 152 sequences (>TrimTree=10) ...

          Loose optimisation of start tree under JC ... done

          Obtaining greedy start tree with 10 sequences ... done

          Reinitialising objects for trimmed data ... done

          New files available: data = </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt.trim.data>; tree = </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt.trim.tree>

Scanning for modelomatic.ini file ... done

Working with genetic code: Universal

>>> Doing model analysis <<< 

RY Done  (1.08313s)

NT Done  (1.18703s)

AA Done  (6.64464s).........

Codon Done  (24.4936s)

Outputting results to </Volumes/Yango/Hayden_batORs/model_o_matic/Phyllos_OR51_Funct_tAlign_mOm_results.txt>

Successful exit

However, word of caution. The "trimfast" option gives a vastly different result:

Normal it is! With fewer parameters, its best just to wait it out.

installing garli on yosemite

sudo gem update --system



brew install open-mpi --cc=gcc-4.9 --build-from-source




brew remove ncl garli



brew install ncl garli --cc=gcc-4.9 --build-from-source