Tag: SATé

PASTA 1.8.6 – Practical Alignment using SATé and TrAnsitivity

PASTA 1.8.6

:: DESCRIPTION

PASTA (Practical Alignment using SATé and TrAnsitivity) is an improvement to SATé: it uses some of the algorithmic design of SATé but is faster, produces more accurate alignments and trees, and can scale to much larger datasets.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Python

:: DOWNLOAD

 PASTA

:: MORE INFORMATION

Citation:

Research in Computational Molecular Biology Lecture Notes in Computer Science Volume 8394, 2014, pp 177-191
PASTA: Ultra-Large Multiple Sequence Alignment
Siavash Mirarab, Nam Nguyen, Tandy Warnow

SATé 2.2.7 – Simultaneous Alignment and Tree Estimation

SATé 2.2.7

:: DESCRIPTION

SATé is a software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data set is divided into smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged for phylogenetic tree inference.

::DEVELOPER

The Holder Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SATé

:: MORE INFORMATION

Citation:

Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder.
“SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees.”
Systematic Biology. 61(1):90-106