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Historic log

VIP Sources

14 sep 2011 3 may 2011 26 oct 2010 19 Ago 2010 20 May 2010

VIP News

14 Sep 2011. A new version of VIP was uploaded
31 Jul 2011. The timed phylogenies approach as well as new searching algorithms were presented at the "XXX meeting of the Willi Hennig Society" at Sao Jose doR Rio Preto, Brazil. The presentation was awarded with the Willi Hennig Student Award (1st place).
3 May 2011. A new version of VIP was uploaded
26 April 2011. Spatial Analysis of Vicariance paper, online in Cladistics
26 October 2010. A new version of VIP was uploaded
19 August 2010. A new version of VIP was uploaded
27 June 2010. Mark Siddall present the method at the "Evolution 2010", at Portland, USA. Thank you Mark!
24 May 2010. VIP method and program was presented at the "XXIX meeting of the Willi Hennig Society", at Honolulu, USA. The presentation was awarded with the Lars Brundin Student Award (2nd place).
20 May 2010. VIP goes available online.
12 May 2010. A technical description on basic algorithms used by VIP was presented in the "Primer Congreso Argentino de Bioinformática", at Quilmes, Argentina. The slides are availble here.

VIP Updates

14 sep 2011
New search approaches implemented, including different annealing types, and solutions fusion.
Some details in the timed phylogenies approach were solved.
Simple vector maps in KML and in the map format of NDM can be loaded.

3 May 2011
Partial elimination is modified, instead of remove part of a distribution (which is computationally expensive), the distribution is eliminated from the ancestor of the node, and the distribution is disjunct against the sister group.
A bug that ignores the metadata of xml files was fixed.
The whole time calibrated phylogenies interface was modified and restructured.
Annealing searches were reconfigured, so they are more efficent now.
It is possible to export grid matrices for NDM, or for excel, with different options.
Overlap is measured against the sister group, and the descendants of a syster group, this is to avoid a double inference of the same barrier.
The node optimization is rewritten, so now it is more modular and easier to maintain.
Support values (analogous to Bremer support [2]) are implemented. They are calculated during search.

26 October 2010
Use of time calibrated phylogenies is allowed. The method uses an approach derived from [1] (Arias, in prep.).
If overlap is produced by filled cells (i.e. no cell in the overlap region has an observed record), then no overlap is measured.
Two kind of neighborhoods are using now for filling, the Moore neighborhood (the one present in the previous versions, based on Chebyshev distance), and von Neumann neighborhood (based on Manhattan distance).
The module calculating the barrier was completely rewritten. It removes the occasional miscalculation that produce loops in the previous versions. Also, it takes into account records on both sides of the Monday/Sunday line.
Several user oriented capabilities (for example, save graphics of actual output) are implemented.

19 August 2010
Search interface was improved, adding a basic searching algorithm (Node flipping), and two searching strategies (sectors, annealing).
It is possible to set cell filling on each terminal individually (this will be useful if the data set includes terminals with restricted distributions as well as terminals with widespread distributions).
Some minor bugs on file reading are fixed.
Now it is possible to save an alphabetic list of the terminals included in the analysis, and the collections (for citation purpouse).
It is possible to save just the terminals with data.


[1] Hunn, C.A., Upchurch, P. 1978. The importance of time/space in diagnosing the causality of phylogenetic events: Towards a 'chronobiogeographical' paradigm? Systematic Biology 50: 391. DOI:10.1093/sysbio/50.3.391.
[2] Bremer, K. 1988. The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803. JSTOR: 2498870.

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