Reformatting

T_Coffee provides also a tool box for cleaning, trimming, reformating or comparing your data: fasta files, multiple sequences alignments, trees (Newick format), structure files etc... It can be used for pre-processing as post-processing steps.

t_coffee -other_pg "command"


 1) Changing the format of your sequences or alignments:
"Changing from a clustalw format to fasta, phylip..."
t_coffee -other_pg seq_reformat -in sh3.aln -output fasta_aln > sh3_fasta.aln



t_coffee -other_pg seq_reformat -in sh3.aln -output phylip_aln > sh3_phylip.aln

"Removing gaps from an alignment (MSA -> dataset) "
t_coffee -other_pg seq_reformat -in sh3.aln -output fasta_seq


2) Trimming alignments:
"Keep only sequences with less than 90% identity..."
t_coffee -other_pg seq_reformat -in sh3.fasta -action +trim _seq_%%90_
"Removing outliers with less than 30% identity with all sequences.."
t_coffee -other_pg seq_reformat -in sh3.fasta -action +trim _seq_%%90_O30

"Keep only 10 sequences more informative..."
t_coffee -other_pg seq_reformat -in sh3.fasta -action +trim _seq_n10_
"Keep the 20% more informative sequences..."
t_coffee -other_pg seq_reformat -in sh3.fasta -action +trim _seq_N20_

"Keep columns with less than 50% gaps..."
t_coffee -other_pg seq_reformat -in sh3.fasta -action +rm_gap 50


3) Extracting information...
"Extracting fasta sequence from a PDB file..."
t_coffee -other_pg extract_from_pdb 1PHT.pdb -fasta

"Extracting block 10 to 20 (respect consensus) ... "
t_coffee -other_pg seq_reformat -in sh3.aln -action +extract_block cons 10 20
"Extracting block 20 to 40 (respect seq 1PHT) ... "
t_coffee -other_pg seq_reformat -in sh3.aln -action +extract_block '1PHT' 20 40


4) Coloring alignments
t_coffee -other_pg seq_reformat -in sh3.aln -action +color_residue 1PHT 10 1 -output color_html > color.html
"Coloring aligment from file ... "
t_coffee -other_pg seq_reformat -in sh3.aln -action +color_residue color.txt -output color_html > file2color.html
"Coloring by conservation ... "
t_coffee -other_pg seq_reformat -in sh3.aln -in3 sh3.aln -action +3evaluate pam250mt -output color_html > cons2color.html



"Coloring by boxshade... "
t_coffee -other_pg seq_reformat -in sh3.aln -in3 sh3.aln -action +3evaluate boxshade -output color_html > boxshade2color.html


5) Comparing/Measuring quality, identity and similarity
"Estimating diversity, average and pairwise identities between sequences in an alignment or dataset..."
t_coffee -other_pg seq_reformat -in sh3.aln -output sim
t_coffee -other_pg seq_reformat -in sh3.fasta -output sim_idscore


"Comparing alignments ... "
t_coffee -other_pg aln_compare -al1 sh3_ref.aln -al2 sh3.aln -compare_mode column



"Comparing trees ... "
t_coffee -other_pg seq_reformat -in crd.struc_tree100 -in2 crd.struc_tree50 -action +tree_cmp