Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics is Highly Beneficial.

Le S.Q., Gascuel O.
Systematic Biology, 59(3): 277-287, 2010

Example

example

Command line

./PhyML-structure -m EX_EHO -M CONF/MIX -i Ord0300_2hhi.STR
Note: PhyML-structure automatically extracts structure information if structure information are put at the end of alignment files. If both alignment files and '-y' option files contain structure information, then PhyML-structure uses the structure in '-y' option.

CONF/MIX

./PhyML-structure -m EX_EHO -M CONF/MIX -i Ord0300_2hhi.STR

Output file: 
. Sequence file : Ord0300_2hhi.STR
. Data set : #1
. Initial tree : user tree (Ord0300_2hhi.STR.tree)
. Model of amino acids substitution: EX_EHO
. Mode: CONF/MIX [Ord0300_2hhi.STR]
. Number of taxa : 10
. Log-likelihood : -2341.10455
. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 3.538
. Confidence    0.592200

------ mixture model in detail -----
Model   Proportion      Pinvar          Rate
E-bur   0.076740        0.000000        0.761817
H-bur   0.009645        0.000000        0.744426
O-bur   0.479179        0.000000        0.532458                    
E-exp   0.058938        0.000000        1.563939
H-exp   0.000299        0.000000        2.064034
O-exp   0.375200        0.000000        1.433368
. Time used 0h0m17s

CONF/LG

./PhyML-structure -m EX_EHO -M CONF/LG -i Ord0300_2hhi.STR

Output file: 
. Sequence file : Ord0300_2hhi.STR
. Data set : #1
. Initial tree : user tree (Ord0300_2hhi.STR.tree)
. Model of amino acids substitution: EX_EHO
. Mode: CONF/LG  [Ord0300_2hhi.STR]
. Number of taxa : 10
. Log-likelihood : -2344.08101
. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 2.572
. Confidence    0.598922
. Time used 0h1m29s
. -> 89 seconds

PART

./PhyML-structure -m EX_EHO -M PART -i Ord0300_2hhi.STR

Output file: 
. Sequence file : Ord0300_2hhi.STR
. Data set : #1
. Initial tree : user tree (Ord0300_2hhi.STR.tree)
. Model of amino acids substitution: EX_EHO
. Mode: PART     [Ord0300_2hhi.STR]
. Number of taxa : 10
. Log-likelihood : -2359.35756
. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 1.882
. Time used 0h0m11s

MIX

./PhyML-structure -m EX_EHO -M MIX -i Ord0300_2hhi.STR

Output file: 
. Sequence file : Ord0300_2hhi.STR
. Data set : #1
. Initial tree : user tree (Ord0300_2hhi.STR.tree)
. Model of amino acids substitution: EX_EHO
. Mode: MIX
. Number of taxa : 10
. Log-likelihood : -2360.83788
. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 4.060

------ mixture model in detail -----
Model   Proportion      Pinvar          Rate
E-bur   0.160239        0.000000        0.761817
H-bur   0.036653        0.000000        0.744426
O-bur   0.182865        0.000000        0.532458
E-exp   0.146034        0.000000        1.563939
H-exp   0.000429        0.000000        2.064034
O-exp   0.473781        0.000000        1.433368
. Time used 0h0m17s