Analyse
bioinformatique des séquences
Exemple d'utilisation de ClustalW pour la phylogénie
lovelace$ clustalw
**************************************************************
******** CLUSTAL W(1.60) Multiple Sequence Alignments ********
**************************************************************
1. Sequence Input From Disc
2. Multiple Alignments
3. Profile / Structure Alignments
4. Phylogenetic trees
S. Execute a system command
H. HELP
X. EXIT (leave program)
Your choice: 1
Sequences should all be in 1 file.
6 formats accepted:
NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF.
Enter the name of the sequence file: xhba
Sequence format is Pearson
Sequences assumed to be DNA
Sequence 1: CHKHBA 541 bp
Sequence 2: DUKHBADWP 513 bp
Sequence 3: SMRHBAA 558 bp
Sequence 4: XELHBA 561 bp
Sequence 5: DAVAGL 547 bp
**************************************************************
******** CLUSTAL W(1.60) Multiple Sequence Alignments ********
**************************************************************
1. Sequence Input From Disc
2. Multiple Alignments
3. Profile / Structure Alignments
4. Phylogenetic trees
S. Execute a system command
H. HELP
X. EXIT (leave program)
Your choice: 2
****** MULTIPLE ALIGNMENT MENU ******
1. Do complete multiple alignment now (Slow/Accurate)
2. Produce guide tree file only
3. Do alignment using old guide tree file
4. Toggle Slow/Fast pairwise alignments = SLOW
5. Pairwise alignment parameters
6. Multiple alignment parameters
7. Reset gaps between alignments? = ON
8. Toggle screen display = ON
9. Output format options
S. Execute a system command
H. HELP
or press [RETURN] to go back to main menu
Your choice: 1
Enter a name for the CLUSTAL output file [xhba.aln]:
Enter name for GUIDE TREE file [xhba.dnd]:
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 59
Sequences (1:3) Aligned. Score: 54
Sequences (1:4) Aligned. Score: 60
Sequences (1:5) Aligned. Score: 61
Sequences (2:3) Aligned. Score: 49
Sequences (2:4) Aligned. Score: 54
Sequences (2:5) Aligned. Score: 59
Guide tree file created: [xhba.dnd]
Start of Multiple Alignment
There are 4 groups
Aligning...
Group 1: Sequences: 2 Score:3345
Group 2: Sequences: 3 Score:3510
Group 3: Sequences: 4 Score:3345
Group 4: Sequences: 5 Score:3221
Alignment Score 19285
Consensus length = 589
CLUSTAL-Alignment file created [xhba.aln]
CLUSTAL W(1.60) multiple sequence alignment
CHKHBA ----------------------ACACAGAGGTGCAACCATGGTGCTGTCCGCTGCTGACA
DUKHBADWP CGCAACCCCGTCAGTTGCCAGCCTGCCACACCGCTGCCGCCATGCTGACCGCCGAGGACA
SMRHBAA -------------------------AACCACCGCAAACATGAAGCTGACTGCCGAAGATA
XELHBA -----------------TGCACAACACAAACAGGAACCATGCTTCTTTCAGCCGATGACA
DAVAGL -----------------------------------------GTGCTCTCGGATGCTGACA
** * * * ** *
......
****** PHYLOGENETIC TREE MENU ******
1. Input an alignment
2. Exclude positions with gaps? = ON
3. Correct for multiple substitutions? = OFF
4. Draw tree now
5. Bootstrap tree
6. Output format options
S. Execute a system command
H. HELP
or press [RETURN] to go back to main menu
Your choice: 4
Enter name for PHYLIP tree output file [xhba.ph]:
Phylogenetic tree file created: [xhba.ph]
****** PHYLOGENETIC TREE MENU ******
1. Input an alignment
2. Exclude positions with gaps? = ON
3. Correct for multiple substitutions? = OFF
4. Draw tree now
5. Bootstrap tree
8 janvier, 2008ystem command
H. HELP
or press [RETURN] to go back to main menu
Your choice: 5
Enter name for bootstrap output file [xhba.phb]
Enter seed no. for random number generator (1..1000) [111]:
Enter number of bootstrap trials (1..10000) [1000]: 100
Each dot represents 10 trials
..........
Bootstrap output file completed [xhba.phb]
lovelace$ more xhba.ph
(
(
CHKHBA:0.16365,
(
SMRHBAA:0.24627,
XELHBA:0.19936)
:0.03571)
:0.01546,
DUKHBADWP:0.18710,
DAVAGL:0.16684);
lovelace$
lovelace$ more xhba.phb
(
(
CHKHBA:0.16365,
(
SMRHBAA:0.24627,
XELHBA:0.19936)
94:0.03571)
78:0.01546,
DUKHBADWP:0.18710,
DAVAGL:0.16684)TRICHOTOMY;
