Test data¶

There are several test sets available:

To run them, just follow the instructions that are given on the README.txt file for each test case.

Specially, take care of the fact that the config file should be edited to put into dir the actual path to the test data directory in your computer.

Modules used¶

The following table summarizes the modules used in each test.

	1a	1b	2a	2b	2c	3a	3b	4	5	6
blastn							X
tblastn							X
tblastx						X	X
add_refs									X
add_taxonomy						X
CGF_and_CGA_CDS_processing						X	X
check_contamination						X
disambiguate						X
merge						X	X
prefix						X
prefix_out						X
remove_stops	X	X	X	X	X	X	X
Clustal_Omega	X	X
Clustal_Omega_codons			X	X	X	X			X	X
T-coffee		X
T-coffee_codons			X
get_phylo_taxa (2 INPUTS)									X
Fasttree	X	X	X				X		X	X
FastRoot		X				X			X	X
Mafft		X
Mafft_codons			X				X
me_tree	X
ml_tree	X
mp_tree					X
MrBayes			X			X
nj_tree	X		X
Probcons		X
Probcons_codons			X
Probcons_refinement		X					X
Rootdigger (2 INPUTS)									X
tree_collapse						X
upgma_tree	X
JModel_test	X		X			X
CGA										X
ipssa								X
kaks				X
split						X

Running times¶

These are the running times for the tests using a high-performance computing server (1TB of RAM with 96 cores, AMD EPYC 7401 24-Core Processor):

Test 1a: ~ 13 minutes.
Test 1b: ~45 minutes.
Test 2a: ~13 minutes.
Test 2b: 3 minutes.
Test 2c: ~9.3 hours.
Test 3a: ~3.8 hours.
Test 3b: ~50 minutes.
Test 4: ~6 minutes.
Test 5: ~17 minutes.
Test 6: ~1.25 hours