http://www.clustal.org/ 以 ClustalW 為主。 = 【安裝】 = {{{ wget http://www.clustal.org/download/current/clustalw-2.0.12-linux-i686-libcppstatic.tar.gz tar zxvf clustalw-2.0.12-linux-i686-libcppstatic.tar.gz }}} = 【測試】 = 1. 指令： {{{ clustalw2 }}} 畫面： {{{ ************************************************************** ******** CLUSTAL 2.0.11 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. 指令 {{{ 1 }}} 畫面 {{{ Sequences should all be in 1 file. 7 formats accepted: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF. Enter the name of the sequence file : }}} 1. 指令 {{{ kinase.tfa }}} 畫面 {{{ Sequence format is Pearson Sequences assumed to be PROTEIN Sequence 1: KAPA_MOUSE 350 aa Sequence 2: KDCA_DROME 354 aa Sequence 3: ARK1_HUMAN 689 aa Sequence 4: KGP2_DROME 1088 aa Sequence 5: YPK2_YEAST 677 aa Sequence 6: VIP_MELGA 444 aa Sequence 7: K6A3_HUMAN 740 aa Sequence 8: DMK_HUMAN 639 aa Sequence 9: KPBG_RABIT 386 aa Sequence 10: KCC1_YEAST 446 aa Sequence 11: PIM1_HUMAN 313 aa Sequence 12: KRAF_DROME 781 aa Sequence 13: TRKB_HUMAN 822 aa Sequence 14: INSR_HUMAN 1382 aa Sequence 15: KPRO_MAIZE 817 aa Sequence 16: DAF1_CAEEL 669 aa ************************************************************** ******** CLUSTAL 2.0.11 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. 指令 {{{ 2 }}} 畫面 {{{ ****** 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 before alignment? = OFF 8. Toggle screen display = ON 9. Output format options I. Iteration = NONE S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: }}} 1. 指令 {{{ 1 }}} 畫面 {{{ Enter a name for the CLUSTAL output file [kinase.aln]: }}} 1. 指令 {{{ 按 Enter }}} 畫面 {{{ Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 45 Sequences (1:3) Aligned. Score: 26 Sequences (1:4) Aligned. Score: 36 ............ Sequences (14:16) Aligned. Score: 11 Sequences (15:16) Aligned. Score: 11 Enter name for new GUIDE TREE file [kinase.dnd]: }}} 1. 指令 {{{ 按 Enter }}} 畫面 {{{ There are 15 groups Start of Multiple Alignment Aligning... Group 1: Delayed Group 2: Sequences: 2 Score:5585 Group 3: Sequences: 2 Score:6757 Group 4: Sequences: 4 Score:4840 Group 5: Sequences: 5 Score:4243 Group 6: Delayed Group 7: Delayed Group 8: Delayed Group 9: Delayed Group 10: Delayed Group 11: Delayed Group 12: Delayed Group 13: Delayed Group 14: Delayed Group 15: Delayed Alignment Score -1627 Consensus length = 1608 CLUSTAL-Alignment file created [kinase.aln] CLUSTAL 2.0.11 multiple sequence alignment KAPA_MOUSE ------------------------------------------------------------ KDCA_DROME ------------------------------------------------------------ YPK2_YEAST ------------------------------------------------------------ VIP_MELGA ------------------------------------------------------------ K6A3_HUMAN ------------------------------------------------------------ PIM1_HUMAN ------------------------------------------------------------ KGP2_DROME MRFCFDRLCFATKRPAQNSNSNAPHSSTTVDAPPRPADVDVATVPVATTAPPPQQPVSNL DMK_HUMAN ------------------------------------------------------------ KPBG_RABIT ------------------------------------------------------------ KCC1_YEAST ------------------------------------------------------------ ARK1_HUMAN ------------------------------------------------------------ INSR_HUMAN ------------------------MGTGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCP TRKB_HUMAN ------------------------------------------------------------ KPRO_MAIZE ------------------------------------------------------------ KRAF_DROME ------------------------------------------------------------ DAF1_CAEEL ------------------------------------------------------------ KAPA_MOUSE ------------------------------------------------------------ Press [RETURN] to continue or X to stop: }}} 1. 指令 {{{ x }}} 畫面 {{{ ****** 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 before alignment? = OFF 8. Toggle screen display = ON 9. Output format options I. Iteration = NONE S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: }}} 1. 指令 {{{ 按 Enter }}} 畫面 {{{ ************************************************************** ******** CLUSTAL 2.0.11 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. 指令： {{{ x }}} 輸出檔案： kinase.aln 、 kinase.dnd 。