test_AlignIO
Testing reading clustal format file Clustalw/cw02.aln with 1 alignments
 Alignment 0, with 2 sequences of length 601
  MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVN...SVV gi|4959044|gb|AAD34209.1|AF069
  ---------MSPQTETKASVGFKAGVKEYKLTYYTP...--- gi|671626|emb|CAA85685.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/opuntia.aln with 1 alignments
 Alignment 0, with 7 sequences of length 156
  TTTTTTT alignment column 0
  AAAAAAA alignment column 1
  TTTTTTT alignment column 2
  AAAAAAA alignment column 3
  CCCCCCC alignment column 4
  ||||||| ...
  AAAAAAA alignment column 155
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/hedgehog.aln with 1 alignments
 Alignment 0, with 5 sequences of length 447
  M---- alignment column 0
  F---- alignment column 1
  N---- alignment column 2
  L---- alignment column 3
  V---- alignment column 4
  ||||| ...
  ---SS alignment column 446
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/odd_consensus.aln with 1 alignments
 Alignment 0, with 2 sequences of length 687
  ------------------------------------...TAG AT3G20900.1-CDS
  ATGAACAAAGTAGCGAGGAAGAACAAAACATCAGGT...TAG AT3G20900.1-SEQ
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-SEQ'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'AT3G20900.' (originally 'AT3G20900.1-SEQ'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/protein.aln with 1 alignments
 Alignment 0, with 20 sequences of length 411
  -M------------------ alignment column 0
  -T------------------ alignment column 1
  -V------------------ alignment column 2
  -L-----------------M alignment column 3
  -E---------------MMS alignment column 4
  |||||||||||||||||||| ...
  -------------------T alignment column 410
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'gi|1377497' (originally 'gi|13774975|gb|AAK39115.1|AF35'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'gi|1377497' (originally 'gi|13774975|gb|AAK39115.1|AF35'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading clustal format file Clustalw/promals3d.aln with 1 alignments
 Alignment 0, with 20 sequences of length 414
  MMMMMMMMMMMMMMMM-M-- alignment column 0
  -----------------T-- alignment column 1
  -----------------V-- alignment column 2
  -----------------L-- alignment column 3
  -S---------------E-- alignment column 4
  |||||||||||||||||||| ...
  -T------------------ alignment column 413
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'gi_1393639' (originally 'gi_13936397_dbj_BAB47195.'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'gi_1393639' (originally 'gi_13936397_dbj_BAB47195.'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta format file GFF/multi.fna with 1 alignments
 Alignment 0, with 3 sequences of length 8
  ACGTCGCG test1
  GGGGCCCC test2
  AAACACAC test3
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading nexus format file Nexus/test_Nexus_input.nex with 1 alignments
 Alignment 0, with 9 sequences of length 48
  AAAAAAAAc alignment column 0
  -----c?tc alignment column 1
  CCCCCCCCc alignment column 2
  --c-?a-tc alignment column 3
  GGGGGGGGc alignment column 4
  ||||||||| ...
  tt--?ag?c alignment column 47
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: t2 the name
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading nexus format file Nexus/codonposset.nex with 1 alignments
 Alignment 0, with 2 sequences of length 22
  AAAAAGGCATTGTGGTGGGAAT Aegotheles
  ?????????TTGTGGTGGGAAT Aerodramus
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading stockholm format file Stockholm/simple.sth with 1 alignments
 Alignment 0, with 2 sequences of length 104
  UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCA...UGU AP001509.1
  AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGA...GAU AE007476.1
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading stockholm format file Stockholm/funny.sth with 1 alignments
 Alignment 0, with 6 sequences of length 43
  MMMEEE alignment column 0
  TQIVVV alignment column 1
  CHEMMM alignment column 2
  RVALLL alignment column 3
  ASDTTT alignment column 4
  |||||| ...
  SYSEEE alignment column 42
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/reference_dna.phy with 1 alignments
 Alignment 0, with 6 sequences of length 13
  CCTTCG alignment column 0
  GGAAAG alignment column 1
  ATAAAC alignment column 2
  TTTTAA alignment column 3
  GAGGAG alignment column 4
  |||||| ...
  CTTTTC alignment column 12
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: B. virgini
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/reference_dna2.phy with 1 alignments
 Alignment 0, with 6 sequences of length 39
  CCTTCG alignment column 0
  GGAAAG alignment column 1
  ATAAAC alignment column 2
  TTTTAA alignment column 3
  GAGGAG alignment column 4
  |||||| ...
  CTTTTC alignment column 38
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: B. virgini
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/hennigian.phy with 1 alignments
 Alignment 0, with 10 sequences of length 40
  CCCCCAAAAA alignment column 0
  AAAAACCCCC alignment column 1
  CCCAAAAAAA alignment column 2
  AAACCAAAAA alignment column 3
  CCAAAAAAAA alignment column 4
  |||||||||| ...
  AAAAAAAAAA alignment column 39
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/horses.phy with 1 alignments
 Alignment 0, with 10 sequences of length 40
  AACCCCCCCC alignment column 0
  AAAACCCCCC alignment column 1
  AAAAAAAAAC alignment column 2
  ACAAAAAAAA alignment column 3
  ACACCCCCCC alignment column 4
  |||||||||| ...
  AAAAAAAAAA alignment column 39
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Failed: Whitespace not allowed in identifier: M. secundu
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/random.phy with 1 alignments
 Alignment 0, with 10 sequences of length 40
  CAAAACAAAC alignment column 0
  AACAACCACC alignment column 1
  CAAAACAAAA alignment column 2
  ACAACACACA alignment column 3
  CCAAAACCAA alignment column 4
  |||||||||| ...
  AAAAAAAAAA alignment column 39
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/interlaced.phy with 1 alignments
 Alignment 0, with 3 sequences of length 384
  -----MKVILLFVLAVFTVFVSS-------------...I-- CYS1_DICDI
  MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPV...VAA ALEU_HORVU
  ------MWATLPLLCAGAWLLGV--------PVCGA...PLV CATH_HUMAN
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip format file Phylip/interlaced2.phy with 1 alignments
 Alignment 0, with 4 sequences of length 131
  TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
  TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
  TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
  TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip-relaxed format file ExtendedPhylip/primates.phyx with 1 alignments
 Alignment 0, with 12 sequences of length 898
  AAAAAAAAAAAA alignment column 0
  AAAAAAAAAAAA alignment column 1
  GGGGGGGGGGGG alignment column 2
  TCCCCCCCCCCC alignment column 3
  TTTTTTTTTTTT alignment column 4
  |||||||||||| ...
  TTTTTTTTTTTT alignment column 897
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip-sequential format file Phylip/sequential.phy with 1 alignments
 Alignment 0, with 3 sequences of length 384
  -----MKVILLFVLAVFTVFVSS-------------...I-- CYS1_DICDI
  MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPV...VAA ALEU_HORVU
  ------MWATLPLLCAGAWLLGV--------PVCGA...PLV CATH_HUMAN
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading phylip-sequential format file Phylip/sequential2.phy with 1 alignments
 Alignment 0, with 4 sequences of length 131
  TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
  TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
  TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
  TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/alignret.txt with 1 alignments
 Alignment 0, with 4 sequences of length 131
  TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
  TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
  TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPG...SHE IXI_236
  TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT-...SHE IXI_237
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/needle.txt with 5 alignments
 Alignment 0, with 2 sequences of length 124
  KILIVDD----QYGIRILLNEVFNKEGYQTFQAANG...--- ref_rec
  -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDG...GET gi|94968718|receiver
 Alignment 1, with 2 sequences of length 119
  KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQAL...--- ref_rec
  -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRAL...LKR gi|94968761|receiver
 Alignment 2, with 2 sequences of length 120
  -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQA...--- ref_rec
  LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAA...HKE gi|94967506|receiver
 ...
 Alignment 4, with 2 sequences of length 125
  KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQAL...--- ref_rec
  TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEAL...KRQ gi|94970041|receiver
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/needle_asis.txt with 1 alignments
 Alignment 0, with 2 sequences of length 3653
  TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTAT...GAA asis
  ------------------------------------...GAA asis
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Failed: Duplicate record identifier: asis
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/water.txt with 1 alignments
 Alignment 0, with 2 sequences of length 131
  TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTG...SHE IXI_234
  TSPASIRPPAGPSSR---------RPSPPGPRRPTG...SHE IXI_235
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/water2.txt with 1 alignments
 Alignment 0, with 2 sequences of length 18
  CGTTTGAGT-CTGGGATG asis
  CGTTTGAGTACTGGGATG asis
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'asis' (originally 'asis'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Failed: Duplicate record identifier: asis
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/matcher_simple.txt with 1 alignments
 Alignment 0, with 2 sequences of length 16
  GPPPQSPDENRAGESS AF069992_1
  GVPPEEAGAAVAAESS CAA85685.1
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading emboss format file Emboss/matcher_pair.txt with 5 alignments
 Alignment 0, with 2 sequences of length 145
  LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFP...SKY HBA_HUMAN
  LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYP...HKY HBB_HUMAN
 Alignment 1, with 2 sequences of length 13
  KKVADALTNAVAH HBA_HUMAN
  QKVVAGVANALAH HBB_HUMAN
 Alignment 2, with 2 sequences of length 18
  KLRVDPVNFKLLSHCLLV HBA_HUMAN
  KVNVDEVGGEALGRLLVV HBB_HUMAN
 ...
 Alignment 4, with 2 sequences of length 10
  VKAAWGKVGA HBA_HUMAN
  VQAAYQKVVA HBB_HUMAN
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output001.m10 with 4 alignments
 Alignment 0, with 2 sequences of length 108
  SGSNT-RRRAISRPVRLTAEED---QEIRKRAAECG...LSR gi|10955263|ref|NP_052604.1|
  AGSGAPRRRGSGLASRISEQSEALLQEAAKHAAEFG...LSR gi|152973457|ref|YP_001338508.1|
 Alignment 1, with 2 sequences of length 64
  AAECGKTVSGFLRAAALGKKVNSLTDDRVLKEV-MR...AIT gi|10955263|ref|NP_052604.1|
  ASRQGCTVGG--KMDSVQDKASDKDKERVMKNINIM...TLT gi|152973588|ref|YP_001338639.1|
 Alignment 2, with 2 sequences of length 38
  MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE gi|10955264|ref|NP_052605.1|
  IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ gi|152973462|ref|YP_001338513.1|
 Alignment 3, with 2 sequences of length 43
  SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEM...TYC gi|10955265|ref|NP_052606.1|
  SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLI...EYC gi|152973545|ref|YP_001338596.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output002.m10 with 6 alignments
 Alignment 0, with 2 sequences of length 88
  SGSNTRRRAISRPVR--LTAEEDQEIRKRAAECG-K...AEV gi|10955263|ref|NP_052604.1|
  SQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRK...VQV gi|162139799|ref|NP_309634.2|
 Alignment 1, with 2 sequences of length 53
  EIRKRAAECGKTVSGFLRAAA-LGKKV----NSLTD...KKL gi|10955263|ref|NP_052604.1|
  EIKPRGTSKGEAIAAFMQEAPFIGRTPVFLGDDLTD...VKI gi|15831859|ref|NP_310632.1|
 Alignment 2, with 2 sequences of length 92
  SEFFSKIESDLKKKKSKGDVFFDLIIPNG-----GK...ATS gi|10955264|ref|NP_052605.1|
  TELNSELAKAMKVDAQRG-AFVSQVLPNSSAAKAGI...QSS gi|15829419|ref|NP_308192.1|
 ...
 Alignment 5, with 2 sequences of length 157
  QYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIASLIN...REI gi|10955265|ref|NP_052606.1|
  EFIRLLSDHDQFEKDQISELTVAANALKLEVAK--N...KKV gi|15833861|ref|NP_312634.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output003.m10 with 3 alignments
 Alignment 0, with 2 sequences of length 55
  ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGG...IAA gi|152973837|ref|YP_001338874.1|
  VRLTAEEDQ--EIRKRAAECG-KTVSGFLRAAALGK...LGA gi|10955263|ref|NP_052604.1|
 Alignment 1, with 2 sequences of length 22
  DDAEHLFRTLSSR-LDALQDGN gi|152973840|ref|YP_001338877.1|
  DDRANLFEFLSEEGITITEDNN gi|10955265|ref|NP_052606.1|
 Alignment 2, with 2 sequences of length 63
  VFGSFEQPKGEHLSGQVSEQ--RDTAFADQNEQVIR...QAM gi|152973841|ref|YP_001338878.1|
  VYTSFN---GEKFSSYTLNKVTKTDEYNDLSELSAS...KGI gi|10955264|ref|NP_052605.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output004.m10 with 1 alignments
 Alignment 0, with 2 sequences of length 102
  AAAAAAGATAAAAAATATCAAATAGAAGCAATAAAA...TCA ref|NC_002127.1|:c1351-971
  AGAGAAAATAAAACAAGTAATAAAATATTAATGGAA...ACA ref|NC_002695.1|:1970775-1971404
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Failed: Repeated name 'ref|NC_002' (originally 'ref|NC_002695.1|:1970775-1971404'), possibly due to truncation
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Failed: Repeated name 'ref|NC_002' (originally 'ref|NC_002695.1|:1970775-1971404'), possibly due to truncation
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output005.m10 with 1 alignments
 Alignment 0, with 2 sequences of length 110
  IKNKDKTLFIVYAT-DIYSPSEFFSKIESDLKKKKS...LSK gi|10955264|ref|NP_052605.1|
  IKDELPVAFCSWASLDLECEVKYINDVTSLYAKDWM...MSE gi|10955282|ref|NP_052623.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output006.m10 with 1 alignments
 Alignment 0, with 2 sequences of length 131
  GCAACGCTTCAAGAACTGGAATTAGGAACCGTGACA...CAT query
  GCAACGCTTCAAGAACTGGAATTAGGAACCGTGACA...CAT gi|116660610|gb|EG558221.1|EG558221
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output007.m10 with 9 alignments
 Alignment 0, with 2 sequences of length 108
  SGSNT-RRRAISRPVRLTAEED---QEIRKRAAECG...LSR gi|10955263|ref|NP_052604.1|
  AGSGAPRRRGSGLASRISEQSEALLQEAAKHAAEFG...LSR gi|152973457|ref|YP_001338508.1|
 Alignment 1, with 2 sequences of length 64
  AAECGKTVSGFLRAAALGKKVNSLTDDRVLKEV-MR...AIT gi|10955263|ref|NP_052604.1|
  ASRQGCTVGG--KMDSVQDKASDKDKERVMKNINIM...TLT gi|152973588|ref|YP_001338639.1|
 Alignment 2, with 2 sequences of length 45
  EIRKRAAECGKTVSGFLRAAA-----LGKKVNSLTD...VMR gi|10955263|ref|NP_052604.1|
  ELVKLIADMGISVRALLRKNVEPYEELGLEEDKFTD...MLQ gi|152973480|ref|YP_001338531.1|
 ...
 Alignment 8, with 2 sequences of length 64
  ISGTYKGIDFLIKLMPSGGNTTIGRASGQNNTYFDE...FSD gi|10955265|ref|NP_052606.1|
  IDGVITAFD-LRTGMNISKDKVVAQIQGMDPVW---...YPD gi|152973505|ref|YP_001338556.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading fasta-m10 format file Fasta/output008.m10 with 12 alignments
 Alignment 0, with 2 sequences of length 65
  LQHRHPHQQQQQQQQQQQQQQQQQQQQQQQQQQQH-...QML sp|Q9NSY1|BMP2K_HUMAN
  IPHQLPHALRHRPAQEAAHASQLHPAQPGCGQPLHG...GLL gi|283855822|gb|GQ290312.1|
 Alignment 1, with 2 sequences of length 201
  GPEIL---LGQ-GPPQQPPQQHRVLQQLQQGDWRLQ...NRS sp|Q9NSY1|BMP2K_HUMAN
  GPELLRALLQQNGCGTQPLRVPTVLPG*AMAVLHAG...QKS gi|57163782|ref|NM_001009242.1|
 Alignment 2, with 2 sequences of length 348
  MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQ...APA sp|P08100|OPSD_HUMAN
  MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQ...APA gi|57163782|ref|NM_001009242.1|
 ...
 Alignment 11, with 2 sequences of length 31
  AQQQESATTQKAEKEVTRMVIIMVIAFLICW sp|P08100|OPSD_HUMAN
  SQQIRNATTMMMTMRVTSFSAFWVVADSCCW gi|283855822|gb|GQ290312.1|
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: We can only write one Alignment to a Nexus file.
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading ig format file IntelliGenetics/VIF_mase-pro.txt with 1 alignments
 Alignment 0, with 16 sequences of length 298
  MMMMMMMMMMMMMMMM alignment column 0
  EEEEEEETEEEENEEE alignment column 1
  NNNNNNNAEEEEQRKK alignment column 2
  --------DEEEEE-- alignment column 3
  --------KKKKKK-- alignment column 4
  |||||||||||||||| ...
  HHHHHHH-AAAAL-R- alignment column 297
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Failed: Need a DNA, RNA or Protein alphabet
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Testing reading pir format file NBRF/clustalw.pir with 1 alignments
 Alignment 0, with 2 sequences of length 2527
  ------------------------------------...--- 804Angiostrongylus_cantonensis
  ------------------------------------...--- 815Parelaphostrongylus_odocoil
 Checking can write/read as 'clustal' format
 Checking can write/read as 'nexus' format
 Checking can write/read as 'phylip' format
 Checking can write/read as 'phylip-relaxed' format
 Checking can write/read as 'phylip-sequential' format
 Checking can write/read as 'stockholm' format
 Checking can write/read as 'fasta' format
 Checking can write/read as 'tab' format
Finished tested reading files
