phylogenetic analysis

Selected Sequence(s)

Sequence	Fasta label (*)	Workbench label (**)
1	1667590	fragment: four-helix bundle,
2	1619604	emb_CAA50662.1_ (X71669) lipid transfer protein [Sorghum bicolor],
3	2407277	emb_CAA50660.1_ (X71667) lipid transfer protein [Sorghum bicolor],
4	1RZL__	emb_CAA80809.1_ (Z23271) lipid transfer protein [Oryza sativa],
5	2407273	gb_AAB70539.1_ (AF017359) lipid transfer protein LPT II [Oryza sativa],
6	951334	gb_AAA74624.1_ (U31766) lipid transfer protein precursor [Oryza sativa],
7	510337	emb_CAA50661.1_ (X71668) lipid transfer protein [Sorghum bicolor],
8	695760	gb_AAB06443.1_ (U66105) phospholipid transfer protein [Zea mays],
9	311331	gb_AAB18815.1_ (U77295) lipid transfer protein [Oryza sativa],
10	311333	gb_AAB70541.1_ (AF017361) lipid transfer protein LPT IV [Oryza sativa],
11	1498597	emb_CAA69949.1_ (Y08691) lipid transfer protein [Oryza sativa]

(*) Clustalw cuts off Fasta labels after the first space (e.g. ">abc def" becomes ">abc").

(**) The Workbench labels ONLY are meaningful if they were formed correctly, which means each label corresponds with the sequence IN THE SAME order in the sequence alignment. This will not always be the case, so use this column carefully.

PHYLIP rooted tree -Phenogram

tree1.gif (5153 bytes)

PHYLIP unrooted tree

tree2.gif (3430 bytes)

Raw Phylip format tree

(
(
1667590:0.00000,
1619604:0.00000)
:0.01052,
2407277:0.02396,
(
1RZL__:-0.03183,
(
(
(
2407273:0.01651,
951334:0.00891)
:0.01233,
510337:0.01342)
:0.09116,
(
(
(
695760:-0.01024,
311331:0.04984)
:0.02403,
311333:0.09466)
:0.03058,
1498597:0.10123)
:0.10184)
:0.05115)
:0.03148);

Citation

Algorithm Citation:
Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Computer Applications in the Biosciences (CABIOS), 8(2):189-191.

Thompson J.D., Higgins D.G., Gibson T.J. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 22:4673-4680(1994).

Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Program Citation:
CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications.

PHYLIP: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.