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author itaxotools
date Sun, 29 Jan 2023 16:24:30 +0000
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1 ASAP command line: Brief Install and How to Description
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5 ******Install
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6 you can install in 4 steps by typing the 4 following commands in a terminal
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7 1) cd <dir where asap.tgz is located>
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8 2) tar -xvzf asap.tgz
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9 3) cd asap
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10 4) make
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11 5) make clean
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12 You should have a working asap script in your asap directory.
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13
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14 ******Run:
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15 If you are in a hurry and want as soon as possible to see asap working, just type
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16
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17 ./asap <file_name>
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20 <file_name> must be one of these files:
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21 -fasta alignment
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22 -phylip distance file
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23 -MEGA distance file (see MEGA information below)
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24
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25 ./asap -h
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26 will give you this help
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27 -h : this help
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28 -r # : nbr of replicates for statistical tests (default is 10^4)
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29 -b # : nbr of best results to be reported (default is 10)
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30 -m : if present the distance Matrix is supposed to be MEGA CVS (other formats are guessed)
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31 -a : output all files: all probabilities, tree and graph files (default only graph files and 10 best agglomerations)
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32 -d # : distance (0: Kimura-2P, 1: Jukes-Cantor --default--, 2: Tamura-Nei 3:simple distance)
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33 -o # : NOT WORKING YET existent directory where results files are written (default is same dir than alignment)
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34 -t # : transition/transversion (for Kimura) default:2
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38
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39 ******Results:
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40 ASAP will print on screen the number of best results you choosed with -b option or the 10 best if no value is specified
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41 It will produce some other files as 2 graphics files
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42
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43
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44 ******Information
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45
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46 This software is delivered with BIONJ C source code very slightly modified to construct the newick tree.
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47
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48 You can get more information on BIONJ here:
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49 BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data."
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50 Gascuel O. Molecular Biology and Evolution. 1997 14:685-695
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51
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53
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54 -------------------MEGA information---------------
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55 Two MEGA distance files are read:
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56
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57 *********
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58 CVS file (default MEGA 5) formated as follows:
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59 [name 1],,
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60 [name 2],##,,
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61 ...
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62 [name n],##,##,... ##,,
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63
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64 You must specify a -m option on command line with this type of file
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65
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66 **********
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67 default MEGA 4, formated as below
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68 #mega
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69 !Format DataType=Distance DataFormat=LowerLeft NTaxa=100
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70 !other informations
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71 line
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72 line...
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73
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74 ;
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75 [1] #name 1
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76 [2] #name 2
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77 ...
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78 [n] #name n
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79
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80 [1 2.... n]
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81 [1]
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82 [2] ##
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83 [3] ## ##
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84 ...
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85 [n] ## ## .....##
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86
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87 This mega format is assumed as soon as the "#mega" keyword is present on 1st line
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88 Some variations are tolerated in this latter format, but if you get an error you should try to stick to one above.