CLUSTALW

-bash-3.2# clustalw -infile=test.seq -outfile=test.msf

 CLUSTAL W (1.83) Multiple Sequence Alignments

Sequence format is Pearson
Sequence 1: gi|5986|emb|Z14321.1|Z14321      380 bp
Sequence 2: gi|5987|emb|Z14322.1|Z14322      242 bp

[snip]

Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  15
Sequences (1:3) Aligned. Score:  6

[snip]

Sequences (7:8) Aligned. Score:  14
Guide tree        file created:   [test.dnd]
Start of Multiple Alignment
There are 7 groups
Aligning...
Group 1:                     Delayed

[snip]

Alignment Score 7959
CLUSTAL-Alignment file created  [test.msf]


-bash-3.2# head -22 test.msf 
CLUSTAL W (1.83) multiple sequence alignment


gi|5987|emb|Z14322.1|Z14322      --------------------------CAAGTNAGNGGTAAAATGAACCCC
gi|5991|emb|Z14326.1|Z14326      GAGATGTCCTTGGCATTTAGAACCCTTTCGTTCGGTATTAAAAGATCACA
gi|5986|emb|Z14321.1|Z14321      ----------------CTTGAAGTTNTCGATAACAAATTTNTNATCCCAG
gi|5990|emb|Z14325.1|Z14325      --------CCAAGTTTGAGATGCATCTCCTTGCACTATTTATAGTGCTCT
gi|5989|emb|Z14324.1|Z14324      -------------------CAAGTNTGAGCCATGAAACTACTTCTNCTGG
gi|5993|emb|Z14328.1|Z14328      -------------------------------ACAAGATCGGAACCACCAA
gi|5992|emb|Z14327.1|Z14327      -------------------------------CAAGTNTGAGGAAAAAAAA
gi|5988|emb|Z14323.1|Z14323      --------------------------------TGGAATGCGCTCTATTCC
                                                                                   

gi|5987|emb|Z14322.1|Z14322      GCTGCTTTNTCGGCATTCACACGATCTCTACTATTCAATCG---ATGCTC
gi|5991|emb|Z14326.1|Z14326      ACCGAAAAAGAAAGATGCCGATGATCTTAACAAAAAGAAAG---A-ACTA
gi|5986|emb|Z14321.1|Z14321      AGAGAAAAGTGAACGAGGAGCCAATGTTTGCAGCGGANACGTTTACTCGA
gi|5990|emb|Z14325.1|Z14325      TTCTCTCACCA-----CCGGCCGTTCTTGGCGGAGCAGAAGTNTTTGAAA
gi|5989|emb|Z14324.1|Z14324      CTCTNTNTCTGAGCA--TATCCGCAAGTTGCCTTGCAGAAGATATAACAA
gi|5993|emb|Z14328.1|Z14328      CCGTGGAATCGGACCAACCTACAGCTCGANATGCTTCANANATGGAATCC
gi|5992|emb|Z14327.1|Z14327      TGATTGGAAGAATCANTCAGCCGCTCCTCAACACCTCACAGAAATTCATG
gi|5988|emb|Z14323.1|Z14323      NNNNCGTGGCACTTTTGCTTTTTAGTGCATTTATCACTTTGGTCGTTTCC
 
                                                                                  
GENEWISE

# ./bin/genewise test_data/road.pep test_data/hn_est.fa 
genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright

Query protein:       roa1_drome
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      hs_est
Strand:              forward
Start/End (protein)  default
Gene Paras:          human.gf
Codon Table:         codon.table
Subs error:          1e-05
Indel error:         1e-05
Model splice?        model
Model codon bias?    flat
Model intron bias?   tied
Null model           syn
Algorithm            623
GeneWise6 Matrix calculation: [ 174000] Cells 99%

genewise output
Score 172.81 bits over entire alignment
Scores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info

roa1_drome        22 DSITEPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKDPRTKR 
                     +S  EPE +RKLFIGGL + TTDE+L++HFE+WG + D VV +DP TKR 
                     ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV!RDPNTKR 
hs_est           117 gtcagcgccaactaggtatgaaggacaactgctgacagtgg2agcaaac 
                     accaacaatgatttggtgtaccaagtggataaggctcagtt gacacag 
                     gttagcaggggcctaggctaattgcggcttgagagcgctga ataccgc 


roa1_drome        71 SRGFGFITYSHSSMIDEAQKSRPHKIDGRVVEPKRAVPRQDIDSPNAGA 
                     SRGFGF+TY+    +D A  +RPHK+DGRVVEPKRAV R+D   P A   
                     SRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 
hs_est           263 tagtgtgatgagggggggaagaccagggagggcaaggtaggtcacggct 
                     cggtgttcacctaatacctacgcaataggttacagctcgaacagcgcat 
                     tgctgtcatctggggtatgtagacggtaatgaagatccaattaaatcca 


roa1_drome       120 TVKKLFVGALKDDHDEQSIRDYF                           
                     TVKK+FVG +K+D +E  +RDYF                           
                     TVKKIFVGGIKEDTEEHHLRDYF                           
hs_est           410 agaaatgggaaggaggcccagtt                           
                     ctaatttggtaaacaaaatgaat                           
                     tgagatttctaactaatcaattt                           


//


BLASTZ

# ./blastz mouse human
#:lav
d {
  "blastz.v7 mouse human
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
  O = 400, E = 30, K = 3000, L = 3000, M = 0"
}
#:lav
s {
  "mouse" 1 10000 0 1
  "human" 1 10001 0 1
}