Running mscore to get scores of alignments ...
/home/goetz/multal/alcompar/alignments/clustalx/ref1/test1
File: 1aab_ref1.msf
File: 1aboA_ref1.msf
File: 1aho_ref1.msf
File: 1csp_ref1.msf
File: 1csy_ref1.msf
File: 1dox_ref1.msf
File: 1fjlA_ref1.msf
File: 1fkj_ref1.msf
File: 1fmb_ref1.msf
File: 1hfh_ref1.msf
File: 1hpi_ref1.msf
File: 1idy_ref1.msf
File: 1krn_ref1.msf
File: 1pfc_ref1.msf
File: 1plc_ref1.msf
File: 1r69_ref1.msf
File: 1tgxA_ref1.msf
File: 1tvxA_ref1.msf
File: 1ubi_ref1.msf
File: 1wit_ref1.msf
File: 1ycc_ref1.msf
File: 2fxb_ref1.msf
File: 2mhr_ref1.msf
File: 2trx_ref1.msf
File: 3cyr_ref1.msf
File: 451c_ref1.msf
File: 9rnt_ref1.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref1/test2
File: 1ad2_ref1.msf
File: 1amk_ref1.msf
File: 1ar5A_ref1.msf
File: 1aym3_ref1.msf
File: 1bbt3_ref1.msf
File: 1ezm_ref1.msf
File: 1gdoA_ref1.msf
File: 1havA_ref1.msf
File: 1ldg_ref1.msf
File: 1led_ref1.msf
File: 1mrj_ref1.msf
File: 1pgtA_ref1.msf
File: 1pii_ref1.msf
File: 1ppn_ref1.msf
File: 1pysA_ref1.msf
File: 1sbp_ref1.msf
File: 1thm_ref1.msf
File: 1tis_ref1.msf
File: 1ton_ref1.msf
File: 1uky_ref1.msf
File: 1zin_ref1.msf
File: 2cba_ref1.msf
File: 2hsdA_ref1.msf
File: 2pia_ref1.msf
File: 3grs_ref1.msf
File: 5ptp_ref1.msf
File: kinase_ref1.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref1/test3
File: 1ac5_ref1.msf
File: 1ad3_ref1.msf
File: 1adj_ref1.msf
File: 1ajsA_ref1.msf
File: 1bgl_ref1.msf
File: 1cpt_ref1.msf
File: 1dlc_ref1.msf
File: 1eft_ref1.msf
File: 1fieA_ref1.msf
File: 1gowA_ref1.msf
File: 1gpb_ref1.msf
File: 1gtr_ref1.msf
File: 1lcf_ref1.msf
File: 1lvl_ref1.msf
File: 1pamA_ref1.msf
File: 1ped_ref1.msf
File: 1pkm_ref1.msf
File: 1rthA_ref1.msf
File: 1sesA_ref1.msf
File: 1taq_ref1.msf
File: 2ack_ref1.msf
File: 2myr_ref1.msf
File: 3pmg_ref1.msf
File: 4enl_ref1.msf
File: actin_ref1.msf
File: arp_ref1.msf
File: gal4_ref1.msf
File: glg_ref1.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref2/test
File: 1aboA_ref2.msf
File: 1ajsA_ref2.msf
File: 1cpt_ref2.msf
File: 1csy_ref2.msf
File: 1havA_ref2.msf
File: 1idy_ref2.msf
File: 1lvl_ref2.msf
File: 1pamA_ref2.msf
File: 1ped_ref2.msf
File: 1r69_ref2.msf
File: 1sbp_ref2.msf
File: 1tgxA_ref2.msf
File: 1tvxA_ref2.msf
File: 1ubi_ref2.msf
File: 1uky_ref2.msf
File: 1wit_ref2.msf
File: 2hsdA_ref2.msf
File: 2myr_ref2.msf
File: 2pia_ref2.msf
File: 2trx_ref2.msf
File: 3grs_ref2.msf
File: 4enl_ref2.msf
File: kinase_ref2.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref3/test
File: 1ajsA_ref3.msf
File: 1idy_ref3.msf
File: 1pamA_ref3.msf
File: 1ped_ref3.msf
File: 1r69_ref3.msf
File: 1ubi_ref3.msf
File: 1uky_ref3.msf
File: 1wit_ref3.msf
File: 2myr_ref3.msf
File: 2pia_ref3.msf
File: 4enl_ref3.msf
File: kinase_ref3.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref4/test
File: 1ckaA_ref4.msf
File: 1csp_ref4.msf
File: 1dynA_ref4.msf
File: 1lkl_ref4.msf
File: 1mfa_ref4.msf
File: 1pfc_ref4.msf
File: 1pysA_ref4.msf
File: 1vln_ref4.msf
File: 1ycc_ref4.msf
File: 2abk_ref4.msf
File: kinase1_ref4.msf
File: kinase2_ref4.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref5/test
File: 1eft_ref5.msf
File: 1ivy_ref5.msf
File: 1pysA_ref5.msf
File: 1qpg_ref5.msf
File: 1thm1_ref5.msf
File: 1thm2_ref5.msf
File: 2cba_ref5.msf
File: S51_ref5.msf
File: S52_ref5.msf
File: kinase1_ref5.msf
File: kinase2_ref5.msf
File: kinase3_ref5.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test
File: ank_ref6.msf
File: ank_ref6_centre.msf
File: apo_ref6.msf
File: apo_ref6_centre.msf
File: dead_ref6.msf
File: dead_ref6_centre.msf
File: faa_ref6.msf
File: faa_ref6_centre.msf
File: ion_ref6.msf
File: ion_ref6_centre.msf
File: kringle_ref6.msf
File: kringle_ref6_centre.msf
File: ktn+trk_ref6.msf
File: lrr_ref6_centre.msf
File: myb_ref6.msf
File: myb_ref6_centre.msf
File: sushi_ref6.msf
File: sushi_ref6_centre.msf
File: trk_ref6.msf
File: trk_ref6_centre.msf
File: zf_ref6.msf
File: zf_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_1a
File: dead_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_1b
File: dead_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_2a
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_2b
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: ank_3_ref6.msf
File: ank_4_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_2c
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: dead_ref6.msf
File: faa_1_ref6.msf
File: faa_2_ref6.msf
File: faa_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: ktn+trk_1_ref6.msf
File: ktn+trk_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_3_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_3
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: dead_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: sh3_ref6.msf
File: sushi_1_ref6.msf
File: sushi_2_ref6.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref6/test_4
File: ank_1_ref6.msf
File: ank_1_ref6_centre.msf
File: ank_2_ref6.msf
File: ank_2_ref6_centre.msf
File: lrr_2_ref6.msf
File: lrr_2_ref6_centre.msf
File: lrr_3_ref6.msf
File: lrr_3_ref6_centre.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_2_ref6_centre.msf
File: sushi_1_ref6.msf
File: sushi_1_ref6_centre.msf
File: sushi_2_ref6.msf
File: sushi_2_ref6_centre.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
File: zf_2_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref7/test
File: 7tm_ref7.msf
File: Nat_ref7.msf
File: acr_ref7.msf
File: dtd_ref7.msf
File: ion_ref7.msf
File: msl_ref7.msf
File: photo_ref7.msf
File: ptga_ref7.msf
/home/goetz/multal/alcompar/alignments/clustalx/ref8/test
File: cellulase_1_ref8.msf
File: cellulase_2_ref8.msf
File: gsh_1_ref8.msf
File: gsh_2_ref8.msf
File: lectin_1_ref8.msf
File: lectin_2_ref8.msf
File: ptga_1_ref8.msf
File: ptga_2_ref8.msf
File: sh3+sh2_1_ref8.msf
File: sh3+sh2_2_ref8.msf
/home/goetz/multal/alcompar/alignments/msa/ref1/test1
File: 1aab_ref1.msf
File: 1aboA_ref1.msf
File: 1aho_ref1.msf
File: 1csp_ref1.msf
File: 1csy_ref1.msf
File: 1dox_ref1.msf
File: 1fjlA_ref1.msf
File: 1fkj_ref1.msf
File: 1fmb_ref1.msf
File: 1hfh_ref1.msf
File: 1hpi_ref1.msf
File: 1idy_ref1.msf
File: 1krn_ref1.msf
File: 1pfc_ref1.msf
File: 1plc_ref1.msf
File: 1r69_ref1.msf
File: 1tgxA_ref1.msf
File: 1tvxA_ref1.msf
File: 1ubi_ref1.msf
File: 1wit_ref1.msf
File: 1ycc_ref1.msf
File: 2fxb_ref1.msf
File: 2mhr_ref1.msf
File: 2trx_ref1.msf
File: 3cyr_ref1.msf
File: 451c_ref1.msf
File: 9rnt_ref1.msf
/home/goetz/multal/alcompar/alignments/msa/ref1/test2
File: 1ad2_ref1.msf
File: 1amk_ref1.msf
File: 1ar5A_ref1.msf
File: 1aym3_ref1.msf
File: 1ezm_ref1.msf
File: 1gdoA_ref1.msf
File: 1ldg_ref1.msf
File: 1led_ref1.msf
File: 1mrj_ref1.msf
File: 1pgtA_ref1.msf
File: 1pii_ref1.msf
File: 1ppn_ref1.msf
File: 1pysA_ref1.msf
File: 1thm_ref1.msf
File: 1tis_ref1.msf
File: 1ton_ref1.msf
File: 1zin_ref1.msf
File: 5ptp_ref1.msf
/home/goetz/multal/alcompar/alignments/msa/ref1/test3
File: 1ad3_ref1.msf
File: 1adj_ref1.msf
File: 1fieA_ref1.msf
File: 1gpb_ref1.msf
File: 1gtr_ref1.msf
File: 1lcf_ref1.msf
File: 1rthA_ref1.msf
File: 1sesA_ref1.msf
File: 3pmg_ref1.msf
File: actin_ref1.msf
/home/goetz/multal/alcompar/alignments/msa/ref2/test
File: 1aboA_ref2.msf
File: 1csy_ref2.msf
File: 1tvxA_ref2.msf
File: 1ubi_ref2.msf
/home/goetz/multal/alcompar/alignments/msa/ref3/test
File: *.msf
FATAL:Additional parameters given!?
FATAL:Additional parameters given!?
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Additional parameters given!?
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Additional parameters given!?
FATAL:Additional parameters given!?
/home/goetz/multal/alcompar/alignments/msa/ref4/test
File: 1ycc_ref4.msf
/home/goetz/multal/alcompar/alignments/msa/ref5/test
File: 1thm2_ref5.msf
File: S52_ref5.msf
File: kinase1_ref5.msf
/home/goetz/multal/alcompar/alignments/msa/ref6/test
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_1a
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_1b
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_2a
File: sushi_ref6.msf
/home/goetz/multal/alcompar/alignments/msa/ref6/test_2b
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_2c
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_3
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref6/test_4
File: ank_1_ref6.msf
File: ank_1_ref6_centre.msf
File: ank_2_ref6.msf
File: ank_2_ref6_centre.msf
File: lrr_2_ref6.msf
File: lrr_2_ref6_centre.msf
File: lrr_3_ref6.msf
File: lrr_3_ref6_centre.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_2_ref6_centre.msf
File: sushi_1_ref6.msf
File: sushi_1_ref6_centre.msf
File: sushi_2_ref6.msf
File: sushi_2_ref6_centre.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
File: zf_2_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/msa/ref7/test
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/msa/ref8/test
File: *.msf
FATAL:Additional parameters given!?
FATAL:Exception: IO Error: msf input file: Stream not open!
FATAL:Exception: IO Error: msf input file: Stream not open!
/home/goetz/multal/alcompar/alignments/dialign2/ref1/test1
File: 1aab_ref1.msf
File: 1aboA_ref1.msf
File: 1aho_ref1.msf
File: 1csp_ref1.msf
File: 1csy_ref1.msf
File: 1dox_ref1.msf
File: 1fjlA_ref1.msf
File: 1fkj_ref1.msf
File: 1fmb_ref1.msf
File: 1hfh_ref1.msf
File: 1hpi_ref1.msf
File: 1idy_ref1.msf
File: 1krn_ref1.msf
File: 1pfc_ref1.msf
File: 1plc_ref1.msf
File: 1r69_ref1.msf
File: 1tgxA_ref1.msf
File: 1tvxA_ref1.msf
File: 1ubi_ref1.msf
File: 1wit_ref1.msf
File: 1ycc_ref1.msf
File: 2fxb_ref1.msf
File: 2mhr_ref1.msf
File: 2trx_ref1.msf
File: 3cyr_ref1.msf
File: 451c_ref1.msf
File: 9rnt_ref1.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref1/test2
File: 1ad2_ref1.msf
File: 1amk_ref1.msf
File: 1ar5A_ref1.msf
File: 1aym3_ref1.msf
File: 1bbt3_ref1.msf
File: 1ezm_ref1.msf
File: 1gdoA_ref1.msf
File: 1havA_ref1.msf
File: 1ldg_ref1.msf
File: 1led_ref1.msf
File: 1mrj_ref1.msf
File: 1pgtA_ref1.msf
File: 1pii_ref1.msf
File: 1ppn_ref1.msf
File: 1pysA_ref1.msf
File: 1sbp_ref1.msf
File: 1thm_ref1.msf
File: 1tis_ref1.msf
File: 1ton_ref1.msf
File: 1uky_ref1.msf
File: 1zin_ref1.msf
File: 2cba_ref1.msf
File: 2hsdA_ref1.msf
File: 2pia_ref1.msf
File: 3grs_ref1.msf
File: 5ptp_ref1.msf
File: kinase_ref1.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref1/test3
File: 1ac5_ref1.msf
File: 1ad3_ref1.msf
File: 1adj_ref1.msf
File: 1ajsA_ref1.msf
File: 1bgl_ref1.msf
File: 1cpt_ref1.msf
File: 1dlc_ref1.msf
File: 1eft_ref1.msf
File: 1fieA_ref1.msf
File: 1gowA_ref1.msf
File: 1gpb_ref1.msf
File: 1gtr_ref1.msf
File: 1lcf_ref1.msf
File: 1lvl_ref1.msf
File: 1pamA_ref1.msf
File: 1ped_ref1.msf
File: 1pkm_ref1.msf
File: 1rthA_ref1.msf
File: 1sesA_ref1.msf
File: 1taq_ref1.msf
File: 2ack_ref1.msf
File: 2myr_ref1.msf
File: 3pmg_ref1.msf
File: 4enl_ref1.msf
File: actin_ref1.msf
File: arp_ref1.msf
File: gal4_ref1.msf
File: glg_ref1.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref2/test
File: 1aboA_ref2.msf
File: 1ajsA_ref2.msf
File: 1cpt_ref2.msf
File: 1csy_ref2.msf
File: 1havA_ref2.msf
File: 1idy_ref2.msf
File: 1lvl_ref2.msf
File: 1pamA_ref2.msf
File: 1ped_ref2.msf
File: 1r69_ref2.msf
File: 1sbp_ref2.msf
File: 1tgxA_ref2.msf
File: 1tvxA_ref2.msf
File: 1ubi_ref2.msf
File: 1uky_ref2.msf
File: 1wit_ref2.msf
File: 2hsdA_ref2.msf
File: 2myr_ref2.msf
File: 2pia_ref2.msf
File: 2trx_ref2.msf
File: 3grs_ref2.msf
File: 4enl_ref2.msf
File: kinase_ref2.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref3/test
File: 1ajsA_ref3.msf
File: 1idy_ref3.msf
File: 1pamA_ref3.msf
File: 1ped_ref3.msf
File: 1r69_ref3.msf
File: 1ubi_ref3.msf
File: 1uky_ref3.msf
File: 1wit_ref3.msf
File: 2myr_ref3.msf
File: 2pia_ref3.msf
File: 4enl_ref3.msf
File: kinase_ref3.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref4/test
File: 1ckaA_ref4.msf
File: 1csp_ref4.msf
File: 1dynA_ref4.msf
File: 1lkl_ref4.msf
File: 1mfa_ref4.msf
File: 1pfc_ref4.msf
File: 1pysA_ref4.msf
File: 1vln_ref4.msf
File: 1ycc_ref4.msf
File: 2abk_ref4.msf
File: kinase1_ref4.msf
File: kinase2_ref4.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref5/test
File: 1eft_ref5.msf
File: 1ivy_ref5.msf
File: 1pysA_ref5.msf
File: 1qpg_ref5.msf
File: 1thm1_ref5.msf
File: 1thm2_ref5.msf
File: 2cba_ref5.msf
File: S51_ref5.msf
File: S52_ref5.msf
File: kinase1_ref5.msf
File: kinase2_ref5.msf
File: kinase3_ref5.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test
File: ank_ref6.msf
File: ank_ref6_centre.msf
File: apo_ref6.msf
File: apo_ref6_centre.msf
File: dead_ref6.msf
File: dead_ref6_centre.msf
File: faa_ref6.msf
File: faa_ref6_centre.msf
File: ion_ref6.msf
File: ion_ref6_centre.msf
File: kringle_ref6.msf
File: kringle_ref6_centre.msf
File: ktn+trk_ref6.msf
File: lrr_ref6_centre.msf
File: myb_ref6.msf
File: myb_ref6_centre.msf
File: sushi_ref6.msf
File: sushi_ref6_centre.msf
File: trk_ref6.msf
File: trk_ref6_centre.msf
File: zf_ref6.msf
File: zf_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_1a
File: dead_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_1b
File: dead_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_2a
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_2b
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: ank_3_ref6.msf
File: ank_4_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_2c
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: dead_ref6.msf
File: faa_1_ref6.msf
File: faa_2_ref6.msf
File: faa_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: ktn+trk_1_ref6.msf
File: ktn+trk_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_3_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_3
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: dead_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: sh3_ref6.msf
File: sushi_1_ref6.msf
File: sushi_2_ref6.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref6/test_4
File: ank_1_ref6.msf
File: ank_1_ref6_centre.msf
File: ank_2_ref6.msf
File: ank_2_ref6_centre.msf
File: lrr_2_ref6.msf
File: lrr_2_ref6_centre.msf
File: lrr_3_ref6.msf
File: lrr_3_ref6_centre.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_2_ref6_centre.msf
File: sushi_1_ref6.msf
File: sushi_1_ref6_centre.msf
File: sushi_2_ref6.msf
File: sushi_2_ref6_centre.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
File: zf_2_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref7/test
File: 7tm_ref7.msf
File: Nat_ref7.msf
File: acr_ref7.msf
File: dtd_ref7.msf
File: ion_ref7.msf
File: msl_ref7.msf
File: photo_ref7.msf
File: ptga_ref7.msf
/home/goetz/multal/alcompar/alignments/dialign2/ref8/test
File: cellulase_1_ref8.msf
File: cellulase_2_ref8.msf
File: gsh_1_ref8.msf
File: gsh_2_ref8.msf
File: lectin_1_ref8.msf
File: lectin_2_ref8.msf
File: ptga_1_ref8.msf
File: ptga_2_ref8.msf
File: sh3+sh2_1_ref8.msf
File: sh3+sh2_2_ref8.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref1/test1
File: 1aab_ref1.msf
File: 1aboA_ref1.msf
File: 1aho_ref1.msf
File: 1csp_ref1.msf
File: 1csy_ref1.msf
File: 1dox_ref1.msf
File: 1fjlA_ref1.msf
File: 1fkj_ref1.msf
File: 1fmb_ref1.msf
File: 1hfh_ref1.msf
File: 1hpi_ref1.msf
File: 1idy_ref1.msf
File: 1krn_ref1.msf
File: 1pfc_ref1.msf
File: 1plc_ref1.msf
File: 1r69_ref1.msf
File: 1tgxA_ref1.msf
File: 1tvxA_ref1.msf
File: 1ubi_ref1.msf
File: 1wit_ref1.msf
File: 1ycc_ref1.msf
File: 2fxb_ref1.msf
File: 2mhr_ref1.msf
File: 2trx_ref1.msf
File: 3cyr_ref1.msf
File: 451c_ref1.msf
File: 9rnt_ref1.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref1/test2
File: 1ad2_ref1.msf
File: 1amk_ref1.msf
File: 1ar5A_ref1.msf
File: 1aym3_ref1.msf
File: 1bbt3_ref1.msf
File: 1ezm_ref1.msf
File: 1gdoA_ref1.msf
File: 1havA_ref1.msf
File: 1ldg_ref1.msf
File: 1led_ref1.msf
File: 1mrj_ref1.msf
File: 1pgtA_ref1.msf
File: 1pii_ref1.msf
File: 1ppn_ref1.msf
File: 1pysA_ref1.msf
File: 1sbp_ref1.msf
File: 1thm_ref1.msf
File: 1tis_ref1.msf
File: 1ton_ref1.msf
File: 1uky_ref1.msf
File: 1zin_ref1.msf
File: 2cba_ref1.msf
File: 2hsdA_ref1.msf
File: 2pia_ref1.msf
File: 3grs_ref1.msf
File: 5ptp_ref1.msf
File: kinase_ref1.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref1/test3
File: 1ac5_ref1.msf
File: 1ad3_ref1.msf
File: 1adj_ref1.msf
File: 1ajsA_ref1.msf
File: 1bgl_ref1.msf
File: 1cpt_ref1.msf
File: 1dlc_ref1.msf
File: 1eft_ref1.msf
File: 1fieA_ref1.msf
File: 1gowA_ref1.msf
File: 1gpb_ref1.msf
File: 1gtr_ref1.msf
File: 1lcf_ref1.msf
File: 1lvl_ref1.msf
File: 1pamA_ref1.msf
File: 1ped_ref1.msf
File: 1pkm_ref1.msf
File: 1rthA_ref1.msf
File: 1sesA_ref1.msf
File: 1taq_ref1.msf
File: 2ack_ref1.msf
File: 2myr_ref1.msf
File: 3pmg_ref1.msf
File: 4enl_ref1.msf
File: actin_ref1.msf
File: arp_ref1.msf
File: gal4_ref1.msf
File: glg_ref1.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref2/test
File: 1aboA_ref2.msf
File: 1ajsA_ref2.msf
File: 1cpt_ref2.msf
File: 1csy_ref2.msf
File: 1havA_ref2.msf
File: 1idy_ref2.msf
File: 1lvl_ref2.msf
File: 1pamA_ref2.msf
File: 1ped_ref2.msf
File: 1r69_ref2.msf
File: 1sbp_ref2.msf
File: 1tgxA_ref2.msf
File: 1tvxA_ref2.msf
File: 1ubi_ref2.msf
File: 1uky_ref2.msf
File: 1wit_ref2.msf
File: 2hsdA_ref2.msf
File: 2myr_ref2.msf
File: 2pia_ref2.msf
File: 2trx_ref2.msf
File: 3grs_ref2.msf
File: 4enl_ref2.msf
File: kinase_ref2.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref3/test
File: 1ajsA_ref3.msf
File: 1idy_ref3.msf
File: 1pamA_ref3.msf
File: 1ped_ref3.msf
File: 1r69_ref3.msf
File: 1ubi_ref3.msf
File: 1uky_ref3.msf
File: 1wit_ref3.msf
File: 2myr_ref3.msf
File: 2pia_ref3.msf
File: 4enl_ref3.msf
File: kinase_ref3.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref4/test
File: 1ckaA_ref4.msf
File: 1csp_ref4.msf
File: 1dynA_ref4.msf
File: 1lkl_ref4.msf
File: 1mfa_ref4.msf
File: 1pfc_ref4.msf
File: 1pysA_ref4.msf
File: 1vln_ref4.msf
File: 1ycc_ref4.msf
File: 2abk_ref4.msf
File: kinase1_ref4.msf
File: kinase2_ref4.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref5/test
File: 1eft_ref5.msf
File: 1ivy_ref5.msf
File: 1pysA_ref5.msf
File: 1qpg_ref5.msf
File: 1thm1_ref5.msf
File: 1thm2_ref5.msf
File: 2cba_ref5.msf
File: S51_ref5.msf
File: S52_ref5.msf
File: kinase1_ref5.msf
File: kinase2_ref5.msf
File: kinase3_ref5.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test
File: ank_ref6_centre.msf
File: dead_ref6_centre.msf
File: faa_ref6.msf
File: faa_ref6_centre.msf
File: ion_ref6.msf
File: ion_ref6_centre.msf
File: kringle_ref6.msf
File: kringle_ref6_centre.msf
File: ktn+trk_ref6.msf
File: trk_ref6.msf
File: trk_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_1a
File: dead_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_1b
File: dead_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_2a
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_2b
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: ank_3_ref6.msf
File: ank_4_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_2c
File: ank_1_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: dead_ref6.msf
File: faa_1_ref6.msf
File: faa_2_ref6.msf
File: faa_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: ktn+trk_1_ref6.msf
File: ktn+trk_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_3_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_3
File: ank_2_ref6.msf
File: dead_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: sh3_ref6.msf
File: sushi_1_ref6.msf
File: sushi_2_ref6.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref6/test_4
File: ank_1_ref6.msf
File: ank_1_ref6_centre.msf
File: ank_2_ref6.msf
File: ank_2_ref6_centre.msf
File: lrr_2_ref6.msf
File: lrr_2_ref6_centre.msf
File: lrr_3_ref6.msf
File: lrr_3_ref6_centre.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_2_ref6_centre.msf
File: sushi_1_ref6.msf
File: sushi_1_ref6_centre.msf
File: sushi_2_ref6.msf
File: sushi_2_ref6_centre.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
File: zf_2_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref7/test
File: 7tm_ref7.msf
File: Nat_ref7.msf
File: acr_ref7.msf
File: dtd_ref7.msf
File: ion_ref7.msf
File: msl_ref7.msf
File: photo_ref7.msf
File: ptga_ref7.msf
/home/goetz/multal/alcompar/alignments/TCOFFEE/ref8/test
File: cellulase_1_ref8.msf
File: cellulase_2_ref8.msf
File: gsh_1_ref8.msf
File: gsh_2_ref8.msf
File: lectin_1_ref8.msf
File: lectin_2_ref8.msf
File: ptga_1_ref8.msf
File: ptga_2_ref8.msf
File: sh3+sh2_1_ref8.msf
File: sh3+sh2_2_ref8.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref1/test1
File: 1aab_ref1.msf
File: 1aboA_ref1.msf
File: 1aho_ref1.msf
File: 1csp_ref1.msf
File: 1csy_ref1.msf
File: 1dox_ref1.msf
File: 1fjlA_ref1.msf
File: 1fkj_ref1.msf
File: 1fmb_ref1.msf
File: 1hfh_ref1.msf
File: 1hpi_ref1.msf
File: 1idy_ref1.msf
File: 1krn_ref1.msf
File: 1pfc_ref1.msf
File: 1plc_ref1.msf
File: 1r69_ref1.msf
File: 1tgxA_ref1.msf
File: 1tvxA_ref1.msf
File: 1ubi_ref1.msf
File: 1wit_ref1.msf
File: 1ycc_ref1.msf
File: 2fxb_ref1.msf
File: 2mhr_ref1.msf
File: 2trx_ref1.msf
File: 3cyr_ref1.msf
File: 451c_ref1.msf
File: 9rnt_ref1.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref1/test2
File: 1ad2_ref1.msf
File: 1amk_ref1.msf
File: 1ar5A_ref1.msf
File: 1aym3_ref1.msf
File: 1bbt3_ref1.msf
File: 1ezm_ref1.msf
File: 1gdoA_ref1.msf
File: 1havA_ref1.msf
File: 1ldg_ref1.msf
File: 1led_ref1.msf
File: 1mrj_ref1.msf
File: 1pgtA_ref1.msf
File: 1pii_ref1.msf
File: 1ppn_ref1.msf
File: 1pysA_ref1.msf
File: 1sbp_ref1.msf
File: 1thm_ref1.msf
File: 1tis_ref1.msf
File: 1ton_ref1.msf
File: 1uky_ref1.msf
File: 1zin_ref1.msf
File: 2cba_ref1.msf
File: 2hsdA_ref1.msf
File: 2pia_ref1.msf
File: 3grs_ref1.msf
File: 5ptp_ref1.msf
File: kinase_ref1.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref1/test3
File: 1ac5_ref1.msf
File: 1ad3_ref1.msf
File: 1adj_ref1.msf
File: 1ajsA_ref1.msf
File: 1bgl_ref1.msf
File: 1cpt_ref1.msf
File: 1dlc_ref1.msf
File: 1eft_ref1.msf
File: 1fieA_ref1.msf
File: 1gowA_ref1.msf
File: 1gpb_ref1.msf
File: 1gtr_ref1.msf
File: 1lcf_ref1.msf
File: 1lvl_ref1.msf
File: 1pamA_ref1.msf
File: 1ped_ref1.msf
File: 1pkm_ref1.msf
File: 1rthA_ref1.msf
File: 1sesA_ref1.msf
File: 1taq_ref1.msf
File: 2ack_ref1.msf
File: 2myr_ref1.msf
File: 3pmg_ref1.msf
File: 4enl_ref1.msf
File: actin_ref1.msf
File: arp_ref1.msf
File: gal4_ref1.msf
File: glg_ref1.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref2/test
File: 1aboA_ref2.msf
File: 1ajsA_ref2.msf
File: 1cpt_ref2.msf
File: 1csy_ref2.msf
File: 1havA_ref2.msf
File: 1idy_ref2.msf
File: 1lvl_ref2.msf
File: 1pamA_ref2.msf
File: 1ped_ref2.msf
File: 1r69_ref2.msf
File: 1sbp_ref2.msf
File: 1tgxA_ref2.msf
File: 1tvxA_ref2.msf
File: 1ubi_ref2.msf
File: 1uky_ref2.msf
File: 1wit_ref2.msf
File: 2hsdA_ref2.msf
File: 2myr_ref2.msf
File: 2pia_ref2.msf
File: 2trx_ref2.msf
File: 3grs_ref2.msf
File: 4enl_ref2.msf
File: kinase_ref2.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref3/test
File: 1ajsA_ref3.msf
File: 1idy_ref3.msf
File: 1pamA_ref3.msf
File: 1ped_ref3.msf
File: 1r69_ref3.msf
File: 1ubi_ref3.msf
File: 1uky_ref3.msf
File: 1wit_ref3.msf
File: 2myr_ref3.msf
File: 2pia_ref3.msf
File: 4enl_ref3.msf
File: kinase_ref3.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref4/test
File: 1ckaA_ref4.msf
File: 1csp_ref4.msf
File: 1dynA_ref4.msf
File: 1lkl_ref4.msf
File: 1mfa_ref4.msf
File: 1pfc_ref4.msf
File: 1pysA_ref4.msf
File: 1vln_ref4.msf
File: 1ycc_ref4.msf
File: 2abk_ref4.msf
File: kinase1_ref4.msf
File: kinase2_ref4.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref5/test
File: 1eft_ref5.msf
File: 1ivy_ref5.msf
File: 1pysA_ref5.msf
File: 1qpg_ref5.msf
File: 1thm1_ref5.msf
File: 1thm2_ref5.msf
File: 2cba_ref5.msf
File: S51_ref5.msf
File: S52_ref5.msf
File: kinase1_ref5.msf
File: kinase2_ref5.msf
File: kinase3_ref5.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test
File: ank_ref6.msf
File: ank_ref6_centre.msf
File: apo_ref6.msf
File: apo_ref6_centre.msf
File: dead_ref6.msf
File: dead_ref6_centre.msf
File: faa_ref6.msf
File: faa_ref6_centre.msf
File: ion_ref6.msf
File: ion_ref6_centre.msf
File: kringle_ref6.msf
File: kringle_ref6_centre.msf
File: ktn+trk_ref6.msf
File: myb_ref6.msf
File: myb_ref6_centre.msf
File: sushi_ref6.msf
File: sushi_ref6_centre.msf
File: trk_ref6.msf
File: trk_ref6_centre.msf
File: zf_ref6.msf
File: zf_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_1a
File: dead_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_1b
File: dead_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sushi_ref6.msf
File: zf_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_2a
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_ref6.msf
File: sushi_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_2b
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: ank_3_ref6.msf
File: ank_4_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: apo_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: myb_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_2c
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: apo_1_ref6.msf
File: apo_2_ref6.msf
File: dead_ref6.msf
File: faa_1_ref6.msf
File: faa_2_ref6.msf
File: faa_3_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: ktn+trk_1_ref6.msf
File: ktn+trk_2_ref6.msf
File: myb_1_ref6.msf
File: myb_2_ref6.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_3_ref6.msf
File: trk_ref6.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_3
File: ank_1_ref6.msf
File: ank_2_ref6.msf
File: dead_ref6.msf
File: kringle_1_ref6.msf
File: kringle_2_ref6.msf
File: sh3_ref6.msf
File: sushi_1_ref6.msf
File: sushi_2_ref6.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref6/test_4
File: ank_1_ref6.msf
File: ank_1_ref6_centre.msf
File: ank_2_ref6.msf
File: ank_2_ref6_centre.msf
File: lrr_2_ref6.msf
File: lrr_2_ref6_centre.msf
File: lrr_3_ref6.msf
File: lrr_3_ref6_centre.msf
File: sh3_1_ref6.msf
File: sh3_2_ref6.msf
File: sh3_2_ref6_centre.msf
File: sushi_1_ref6.msf
File: sushi_1_ref6_centre.msf
File: sushi_2_ref6.msf
File: sushi_2_ref6_centre.msf
File: zf_1_ref6.msf
File: zf_2_ref6.msf
File: zf_2_ref6_centre.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref7/test
File: 7tm_ref7.msf
File: Nat_ref7.msf
File: acr_ref7.msf
File: dtd_ref7.msf
File: ion_ref7.msf
File: msl_ref7.msf
File: photo_ref7.msf
File: ptga_ref7.msf
/home/goetz/multal/alcompar/alignments/hmmer/ref8/test
File: cellulase_1_ref8.msf
File: cellulase_2_ref8.msf
File: gsh_1_ref8.msf
File: gsh_2_ref8.msf
File: lectin_1_ref8.msf
File: lectin_2_ref8.msf
File: ptga_1_ref8.msf
File: ptga_2_ref8.msf
File: sh3+sh2_1_ref8.msf
File: sh3+sh2_2_ref8.msf
done.
802.71user 14.51system 14:35.27elapsed 93%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (1399484major+1241913minor)pagefaults 0swaps
