Analyse
bioinformatique des séquences
Exemple de fonctionnement des différents logiciels de phylogénie
dans GCG :
gcg%distances
Distances creates a table of the pairwise distances within a group of
aligned sequences.
DISTANCES for what aligned sequences ? cah.msf{*}
Begin (* 1 *) ?
End (* 321 *) ?
Reading sequences...
cahp_mouse: 321 total, 321 read
cahp_human: 321 total, 321 read
cah5_human: 321 total, 321 read
cah5_mouse: 321 total, 321 read
cah3_mouse: 321 total, 321 read
cah3_rat: 321 total, 321 read
cah3_human: 321 total, 321 read
Distances will be computed for 19 protein sequences.
Which distance correction method to use ?
1 Uncorrected distance
2 Jukes-Cantor distance
3 Kimura protein distance
Choose the method to use: (* 3 *)
What should I call the distance matrix file (* cah.distances *) ?
Computing distances using Kimura method...
1 x 2: 1.75 1 x 3: 138.50
1 x 4: 141.50 1 x 5: 123.16
1 x 6: 119.76 1 x 7: 116.49
1 x 8: 121.44 1 x 9: 107.90
17 x 18: 26.11 17 x 19: 46.46
18 x 19: 39.10
Statistics on pairwise distances:
66 of 171 pairs have distances exceeding 70.0.
GROWTREE
GrowTree creates a phylogenetic tree from a distance matrix created by
Distances using either the UPGMA or neighbor-joining method. You can create
a text or graphics output file.
gcg%growtree -CHE
Minimal Syntax: % growtree [-INfile=]hum_gtr.distances -Default
Prompted Parameters:
[-OUTfile=]hum_gtr.trees output file of tree information in Newick's
8:45 format
-MENu=1 allows choice of neighbor-joining or UPGMA
methods
-DENsity=20.0 number of sequences per 100 pu in the tree plot
Local Data Files: None
Optional Parameters:
-NONEGative resets negative branch lengths to zero
-NOBRanch suppresses reporting branch lengths in trees file
-ROUND reports branch lengths in trees file to nearest integer
-NOPLOt suppresses graphical display of tree
-ORDer=0 method for ordering sequences in tree display
-TREEFORMat=1 format to use in drawing the tree
All GCG graphics programs accept these and other switches. See the Using
Graphics chapter of the USERS GUIDE for descriptions.
-FIGure[=FileName] stores plot in a file for later input to FIGURE
-FONT=3 draws all text on the plot using font 3
-COLor=1 draws entire plot with pen in stall 1
-SCAle=1.2 enlarges the plot by 20 percent (zoom in)
-XPAN=10.0 moves plot to the right 10 platen units (pan right)
-YPAN=10.0 moves plot up 10 platen units (pan up)
-PORtrait rotates plot 90 degrees
Add what to the command line ?
What is the distance matrix ? cah.distances
Which method to use ?
1 Neighbor-joining
2 UPGMA
Choose the method to use: (* 1 *)
What should I call the trees file (* cah.trees *) ?
17 internal, 19 terminal nodes
The minimum density for a one-page plot is 12.7 taxa/100 platen units.
What density do you want (* 12.7 *) ?
That will take 1 page. Is this all right (* yes *) ?
HPGL instructions for a HP7550 are now being sent to PlotPort.
gcg%more cah.trees
#NEXUS
[ Trees from file: cah.distances ]
begin trees;
utree Tree_1 = (((('cahp_mouse':1.22,'cahp_human':0.53):78.67,('cah5_human'
:15.10,'cah5_mouse':20.78):39.97):2.01,((((('cah3_mouse':3.42,
'cah3_rat':3.04):1.80,'cah3_human':5.11):1.55,'cah3_horse'
:5.90):25.53,'cah2_chick':20.75):4.35,(('cah2_bovin':3.73,
'cah2_sheep':5.74):13.67,(('cah2_mouse':3.35,'cah2_rat':4.39)
:11.31,'cah2_rabit':11.75):0.71):8.22):2.57):8.68,(((('cah1_macmu'
:0.41,'cah1_macne':0.36):2.09,'cah1_human':2.50):9.71,'cah1_horse'
:11.25):1.65,'cah1_mouse':13.43):8.68):0.00;
endblock;
gcg%8 janvier, 2008ard
Peut être repris dans NJplot (représentation graphique sur
MAC ou PC distribué avec Clustalw), Treetool, ...
_______________________________________________
Sortie graphique des arbres (et autres graphiques GCG)
Configurer GCG pour avoir une sortie graphique
* tektronix (telnet)
* postscript
Une première fois il est nécessaire d'importer dans le
répertoire principal
(~user) le fichier de configuration des "drivers" graphiques de GCG :
gcg% fetch .gcgmydevices
La sélection du "driver" graphique s'effectue par la commande
setplot
gcg% setplot
choisir la sortie avec les flèches ( [arrowdown] ou [arrowup])
* Transférer le fichier résultat (graphic.ps) avec la
commande ftp et imprimer le avec Drop-PS
