Дополнительные задания.

1)Повторите обязательное упражнение 1 задания 3, использовав jackknife вместо bootstrap (опция "-test j" программы fseqboot).

                       +------F
                +-73.0-|
                |      +------E
         +100.0-|
         |      |      +------A
  +------|      +-99.0-|
  |      |             +------B
  |      |
  |      +--------------------D
  |
  +---------------------------C



Консенсусное дерево:

A B C D E F
. . * * . .   100.00 
* * . . . .   99.00
. . . . * *   73.00

Реальное дерево:

A B C D E F
. . . . * *   73.00
* * . . . .   99.00
. . * * . .   100.00

2)Освойте программу fretree.

  ,---------1:B
  !
  !        ,-----------------2:E
  !        !
--7--------8     ,-------------3:C
  !        !  ,-10
  !        `--9  `--------------4:D
  !           !
  !           `--------------------------------------------------------------5:
  !
  `--------------6:A

  ,-------------------------------------------------------------------------5:F
  !
  !                                                ,------------------------6:A
-11                                  ,-------------7
  !                               ,--8             `-----------------1:B
  !                               !  !
  `-------------------------------9  `------------------------------2:E
                                  !
                                  !   ,-----------------------3:C
                                  `--10
                                      `------------------------4:D

3)Создайте изображение переукорененного дерева из предыдущего упражнения как филограммы (phenogram), ориентированной вправо.

4)Восстановите методом максимального правдоподобия (программой fdnamlk) предковую последовательность для ваших мутированных последовательностей и сравните ее с реальной предковой последовательностью.

Probable sequences at interior nodes:

  node                    Reconstructed sequence (caps if > 0.95)

    5        rtscamwgkk wykccarswc ycctkartac gctstgckgs wracsctggk warcatgcmg
 F           GTCCAAAAGG TTGCCAGGTC CCTTTAACAT GCTGCGCGAG TCGCGCTGGT AACCGTACCG
    2        yTgCaCTGTT AmTCCArCAC tcCtGatTAC GmTsTaCTGC agACCctGGG TAaCAtGyag
    4        tTGCaCTGTT AmTCCAaCAC tcCtGatTAC GmTcTaCTGC agACCctGGG TAaCAtGtag
 E           CAGCTCTGTT ACTGCACGTC GACTGCTTAC GATTTACTGC AGACCATGGC TAACACTGAG
    3        tTGCaCtGTT AaTCCArCAC tcCTGrTTAC GmTcTaCTGC AaACCCgGGG TaaCAtGtag
 D           TTGCCCCGTT AATCCCGCAC GCCTGGTTAC GTTGTACTGC AATCCCGGGG TAACATGTCC
 C           TTGCACTGTT AAACCATCAC TCCTGTTTAC GATCTTCTGC AAAACCGGGG TGGCATGTAA
    1        rTgCAcTGtT AcTCCAaCAC TtCaGagTAC gctcTgCTgC ygACCcTGGG TAgCAaGcaG
 B           GTGCACTGTT AGTCCAACAC TTCAGAGTAC GCGCTGCTCC CGACCCTGGG TAGCAAGCCG
 A           ATACAGTGGT ACTCCAACAC TTCAGAGTAC CCTGTGCTGC TGACCGTGGG TACCAAGCAG

    5        cgycakrskt gtmataacaa rsgttccgwg sccmkccgyg mcaswmkgca tcgckrcsrt
 F           CATCGGGCTT ATAATGACAA AGGTTCTGTG CCTCTCTGCG CCGGACTGCA TCACTTCGTT
    2        CgsCATagkt GtCatAACaA gcgtTCcGAa GCCaGCCGtG AcAcTaggCg TCGcGaCCaT
    4        CgsCATagkt GtCatAACaA gCgTTCcGAa GCCaGCCGtG AcACTaggCg TCGcGaCCaT
 E           AGCCATAGAC GCCACAAATA GCGTTCCGAA GCCACCCGTG ACACTTGGCG TCGCGACCAT
    3        CcsCATagtT GTCATAACaA gCGtTCcGAg GCCaGCCGtG AcActagaCg TCGcGaCCaT
 D           CCCCATGGTT GTCATAACAA GCGTTCTGAG GCCCGCCGCC ATACCAGACG TCGGGTCCAT
 C           CCGCATTTTT CTCATAACTA TCGATCCGAG GCCAGCCGGG ACATTATCCT TCGCGACCGT
    1        CGgCAtAggt GtCctaACAa rcctTccGAa GcCaGcCgTG AcaCTaggCa TcGyGacCaT
 B           CGACATAGGG GGCCACACAA ACCGTGGGAT GTCAGCCGTG ACACTGCACA TCGAGGCCAT
 A           CGGCAGAAGT GTCCTAACAT CTCTTCCGAA GCCTGACATG ATCCTAGGCA TTGTGAACGT

    5        syggassrgg ccatcsassy gcawgwmack mmargrttmr ssgwksrrwy atkwstctat
 F           GTGGAGCGGG CCACCGACCT GCATATCATG ACAGGACTAG CCGATGTCAT GTGACTTCAT
    2        CrGGAcsagG CCATCCAgGc gcAwGaAact cAAmGtTTca gGGtGcaaTk ATTtgtCtAT
    4        CrGGAcsagG CCATCCAgGc gcAwGaAact cAAmGtTTCa gGGtGcaaTk ATTtGtCtAT
 E           CGGCATAATG CCATCCAAGC GCAGGAAATG CATTCTTTCG CGGTGCAAAT CTAAGTCTAT
    3        CygGACgmgG CCATCCaGGc atAtGaAAct CaAaGkTTCa gGGtGcaaTg ATTtgtCtaT
 D           CCAGACGTCG CAATCCGGGT ATTTGACAGT CGAAGGTTCA GTGTGTAGTG ATTAATGAAA
 C           CTGGACCCGT CCATCCAGGG AAATGTAACG CAAAGCTTCA GGGAGACATC ATTTGGCTGT
    1        CaGGACgAGG cCATccAGGc gcAaGrAcCt rAAcGtTtca gGGtGCagTg ATTtGaCtAT
 B           CAGGACCAGG ACATGCAGGA GTAAGCACCT AAACGGTTTA GGGAGCGGTA ATTTGACTAT
 A           CAGGACGAGG CCATCGAGGC TCAAGGACCT GAACGTTACG TGGTGCATTG ATTTGACAAT

    5        wtmcrcwaky wmcwcgrckt rgmyrgcmac gtkktskcmm scaagsakaa tsamkwmrac
 F           TTATACAATC ACCTCGTCGT AGCTTGCAGC GTGTTCTCCC CCAAGCATAA TCAATAAAGC
    2        Atccgctaka tACAcggCtT ggacaGCCAC gtTGTgGCra GCaaGGAgaA tGaCGtCwAc
    4        Atccgctaga tACAcggCtT ggacaGCCAC gtTGTgGCra GCaaGGAgaA tGaCGtCwAc
 E           ATTCAGTAGA TACATGGGCT TAATAGACAC TTTGTACCGA GCAAGTAACA TTACGCCGAC
    3        AtccgCtakA tACAcaaCtT gGacgGCCAC gtTGTGGCya GCaAGGAgAA tGACGtCtAc
 D           AACTGCTCTA TACAGAACGT TGACGGCCAC GCTGTGGCCT GCTAGGAGAA TGACGACTAC
 C           ATACCCCGAA GACACTACTT GGTCGGCCAC GTTGTGGCTA GCAAGGATAA GGACGTAAAG
    1        AyCcgcaAgt tacaCggCTT GgaraGCCAc raTgTGGcaa GcrcGGagaa tGcCgtCtAc
 B           ACCCTCAATT GAACCAGCTT GGAAAGCCAG AATGTGGCAC GCGCGGAGAA GGCCGGCCAC
 A           AGCGGGAAGT TTCACGGCTT GTGGCGCCAC TATCTGGTAA GGTCGGCCGC TGCCTTCTAT

    5        skstcygttg sswctgwaka tywscatawc cycsacgccg rmkkrrskta aagskawawg
 F           CTGTCTGTCG GGACTGTAGA TTACCACAAC CTCGACGCCG TCGGTTCTCG AAGGTGAAAG
    2        sgCTccgTTG CCTcTgAata twtGCatATC caCCacgcCG aattaaGGTa AagcGatATg
    4        sgCTccgTTG CCTcTgAata twTGCATATC CaCCacgcCG aattAAGGTA AagcGAtATg
 E           TTCTCTCTTG CCACTCAATA TCTGGATAGC TCCCAGCCCC AATTAAGCTA AACATATATG
    3        ggCTccGtTG CCTrTraaac twTGCaTATC CaCCACgcCG aaTTAAGGTA AagcGAyATG
 D           GCCTCCGTTG GCTGTTGCAC TGTGCATATC CCCCACGACG CATTAAGGTA ACCTGAGATG
 C           GGCTCCGCTG CATATAAGAC ATTGCCTATA CAGCACCTCG AGTTAATGTA CAGCGACATG
    1        mGCTtcgTtG CCTcTgAATA yatGCataTC CaCCccGCCG aatraaGGTa ArGCGatATy
 B           CGCTTTGTTG CCTCTGAATA CATGCACCTC CACCCCGCCG AAGGAAGGTG ACGCGATATT
 A           AGCTTCATAG CCTTTGAATA GACGCTTATC CACCCTGCCG GTCAGGGGTA AGGCGGAATC

    5        cwmrawkctg gckwgygwga sgwgcasyat tttsmcgatg mygtwmtsgs ykmgsgkggs
 F           CTCTGTTTTG GCTAGTAAGA GAAGCACCAT TCTCCCGGCA CCATACTCGC ATAGGAGGAC
    2        caAaaAGcTG GCgTGaGTGa cGTgCAGtAT TTcGaCGAtg AtGTTATsgG cGCgcgtggg
    4        caAAaAGcTG GCgTGaGTGa CGTgCAGtAT TTcGaCGATG AtGTTATggG cGCgcgtsgg
 E           GTAAGAGCTG GCTTGAGTGA CGTGCAGGAT TTCGACGATG ATGTAATCCG CGCACCAGAG
    3        caAAAAGaTG gcgTGAGTGt cGTgCAGtAT tTcGcCgAtg ATGTTatgGG cGCgcgtsgg
 D           CAAAAATATG ATGTGATAGT TGTACAGCTT TGCGCCGATG ATGATACAGG CGCCAGTCGG
 C           ACAAAAGATG GCGTGAGTGT CGTGCCGTAT CTAGCCAACA ATTTTGTGGG CCCGTATGCT
    1        cAAaAaGCTG GCgTGcGTGA CGtgCAGTAt TTtGAcGATG AgGTTATggG tGCGCGtcGg
 B           TAAGATGCTG GCGTGCGTGA CGGACAGTAT TTTGACGATG AGGTTATGTG TGCGCGCCGT
 A           CAAAAAGCTG GCCTGCGTGA CGTGCAGTAA TTTGAGGATG AGGTTATTGG TGCGCGTTGG

    5        gtkmrastgg tgsmyttgma gtgyckgscg wwgayagkkr gw
 F           GTTAAGCTGG TGGCCTTACA GTACTGGGTG TAGGTGGTGT GT
    2        GtGcgagtgG tgCatTTGaA gtGtCtacCg AtgAcarGTg GA
    4        GtGcgAgTgG tgCAtTTGaA gtGtCTaCCg AtgAcagGTg GA
 E           GAGTGAGCGG TTGATTTGGA ACGTCTACGG ATCCCCAGTG GA
    3        GTGCaarTgG gGCAtTTGaA gtGyCTgcCc aTgAcAgGTg GA
 D           GTGCAGATTG GGCACTTCCA CAGACTGTCC ATGACAGGTG GA
 C           GTGCAATTAG GGCAATTGAA GTGCCTGCCC GTAACAAGTG GT
    1        GtgCgAgTGG tgCaTTTGAA gtGtctaCCG AagAcaggTa GA
 B           GTGCGAGTGG CACGTTTGAA GAGAGTACCG AAGAGATGTA GA
 A           GCCCGACTGG TGCATTTGAA CTGTCCTCCG AAAATTGTTA GA