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| author | itaxotools |
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| date | Sun, 29 Jan 2023 16:24:30 +0000 |
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| 1 ASAP command line: Brief Install and How to Description | |
| 2 | |
| 3 | |
| 4 | |
| 5 ******Install | |
| 6 you can install in 4 steps by typing the 4 following commands in a terminal | |
| 7 1) cd <dir where asap.tgz is located> | |
| 8 2) tar -xvzf asap.tgz | |
| 9 3) cd asap | |
| 10 4) make | |
| 11 5) make clean | |
| 12 You should have a working asap script in your asap directory. | |
| 13 | |
| 14 ******Run: | |
| 15 If you are in a hurry and want as soon as possible to see asap working, just type | |
| 16 | |
| 17 ./asap <file_name> | |
| 18 | |
| 19 | |
| 20 <file_name> must be one of these files: | |
| 21 -fasta alignment | |
| 22 -phylip distance file | |
| 23 -MEGA distance file (see MEGA information below) | |
| 24 | |
| 25 ./asap -h | |
| 26 will give you this help | |
| 27 -h : this help | |
| 28 -r # : nbr of replicates for statistical tests (default is 10^4) | |
| 29 -b # : nbr of best results to be reported (default is 10) | |
| 30 -m : if present the distance Matrix is supposed to be MEGA CVS (other formats are guessed) | |
| 31 -a : output all files: all probabilities, tree and graph files (default only graph files and 10 best agglomerations) | |
| 32 -d # : distance (0: Kimura-2P, 1: Jukes-Cantor --default--, 2: Tamura-Nei 3:simple distance) | |
| 33 -o # : NOT WORKING YET existent directory where results files are written (default is same dir than alignment) | |
| 34 -t # : transition/transversion (for Kimura) default:2 | |
| 35 | |
| 36 | |
| 37 | |
| 38 | |
| 39 ******Results: | |
| 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 | |
| 41 It will produce some other files as 2 graphics files | |
| 42 | |
| 43 | |
| 44 ******Information | |
| 45 | |
| 46 This software is delivered with BIONJ C source code very slightly modified to construct the newick tree. | |
| 47 | |
| 48 You can get more information on BIONJ here: | |
| 49 BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data." | |
| 50 Gascuel O. Molecular Biology and Evolution. 1997 14:685-695 | |
| 51 | |
| 52 | |
| 53 | |
| 54 -------------------MEGA information--------------- | |
| 55 Two MEGA distance files are read: | |
| 56 | |
| 57 ********* | |
| 58 CVS file (default MEGA 5) formated as follows: | |
| 59 [name 1],, | |
| 60 [name 2],##,, | |
| 61 ... | |
| 62 [name n],##,##,... ##,, | |
| 63 | |
| 64 You must specify a -m option on command line with this type of file | |
| 65 | |
| 66 ********** | |
| 67 default MEGA 4, formated as below | |
| 68 #mega | |
| 69 !Format DataType=Distance DataFormat=LowerLeft NTaxa=100 | |
| 70 !other informations | |
| 71 line | |
| 72 line... | |
| 73 | |
| 74 ; | |
| 75 [1] #name 1 | |
| 76 [2] #name 2 | |
| 77 ... | |
| 78 [n] #name n | |
| 79 | |
| 80 [1 2.... n] | |
| 81 [1] | |
| 82 [2] ## | |
| 83 [3] ## ## | |
| 84 ... | |
| 85 [n] ## ## .....## | |
| 86 | |
| 87 This mega format is assumed as soon as the "#mega" keyword is present on 1st line | |
| 88 Some variations are tolerated in this latter format, but if you get an error you should try to stick to one above. |