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TreeTop - Phylogenetic Tree Prediction

    The source sequence multiple alignment could be formed from low and upper case letters. Upper case letters will show that there is a homology between correspondent fragments in alignment.

Use homological
fragments only

Yes No
Scale
Throw off columns with
N unknown nucleotide

Algorithm
Matrix
Start position
End position
Gap penalty (in SD units)
Extra tree format
Picture Options
Picture width

Picture height
Bootstrap
Yes No
Picture formats
Max/min factor for Unrooted 2
cluster algorithm
topoligical algorithm
Alignment example:
Human           -KITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQ
Chicken         -KISVVGVGAVGMACAISILMKDLADELTLVDVVEDKLKGEMMDLQHGSLFLKTPKITSGKDYSVTAHSKLVIVTAGARQ
Dogfish         -KITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQ
Lamprey         SKVTIVGVGQVGMAAAISVLLRDLADELALVDVVEDRLKGEMMDLLHGSLFLKTAKIVADKDYSVTAGSRLVVVTAGARQ
Barley          TKISVIGAGNVGMAIAQTILTQNLADEIALVDALPDKLRGEALDLQHAAAFLPRVRI-SGTDAAVTKNSDLVIVTAGARQ
Maizey          TKVSVIGAGNVGMAIAQTILTRDLADEIALVDAVPDKLRGEMLDLQHAAAFLPRTRLVSGTDMSVTRGSDLVIVTAGARQ
Lacto_casei     -KVILVGDGAVGSSYAYAMVLQGIAQEIGIVDIFKDKTKGDAIDLSNALPFTSPKKIYSA-EYSDAKDADLVVITAGAPQ
Bacillus_stea   -RVVVIGAGFVGASYVFALMNQGIADEIVLIDANESKAIGDAMDFNHGKVFAPKPVDIWHGDYDDCRDADLVVICAGANQ
Lacto_plant     QKVVLVGDGAVGSSYAFAMAQQGIAEEFVIVDVVKDRTKGDALDLEDAQAFTAPKKIYSG-EYSDCKDADLVVITAGAPQ
Therma_mari     MKIGIVGLGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDLIHGTPFTRRANIYAG-DYADLKGSDVVIVAAGVPQ
Bifido          -KLAVIGAGAVGSTLAFAAAQRGIAREIVLEDIAKERVEAEVLDMQHGSSFYPTVSIDGSDDPEICRDADMVVITAGPRQ
Thermus_aqua    MKVGIVGSGFVGSATAYALVLQGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRSGW-YEDLEGARVVIVAAGVAQ
Mycoplasma      -KIALIGAGNVGNSFLYAAMNQGLASEYGIIDINPDFADGNAFDFEDASASLPFPISVSRYEYKDLKDADFIVITAGRPQ

Last updated - May 24, 2001.
Any comments or suggestions are welcomed at: nik@genebee.msu.su