• MUSCLE

  • Referenced in 73 articles [sw13193]
  • fast distance estimation using kmer counting, progressive alignment using a new profile function we call ... expectation score, and refinement using tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE ... CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark...
  • RNAforester

  • Referenced in 7 articles [sw15709]
  • Forest alignment with affine gaps and anchors. We present two enhancements ... Jiang et al.’s tree alignment algorithm [Theor. Comput ... when certain nodes in the trees are pre-aligned by a so-called anchoring. Both ... tool RNAforester. We also argue that tree alignment should be parameterized by a user-described...
  • ViennaRNA

  • Referenced in 22 articles [sw10504]
  • distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide...
  • Bali-phy

  • Referenced in 11 articles [sw16614]
  • Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during...
  • CLUSTAL

  • Referenced in 18 articles [sw12750]
  • microcomputer. An approach for performing multiple alignments of large numbers of amino acid or nucleotide ... based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity ... scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from ... pairwise alignments of clusters of sequences, following the order of branching in the tree...
  • SATe

  • Referenced in 3 articles [sw24610]
  • SATe: SATé - Simultaneous Alignment and Tree Estimation. SATé is a software package for inferring ... tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data ... smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged ... affect version prior to 2.2.2). The alignment and tree searching routines are implemented by calling...
  • FastTree

  • Referenced in 7 articles [sw28979]
  • FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree ... methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized ... reliability of each split in the tree, FastTree computes local support values with the Shimodaira...
  • INDELible

  • Referenced in 7 articles [sw23043]
  • methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome...
  • PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • alignment tool for phylogenetic networks. Phylogenetic networks are a generalization of phylogenetic trees that allow ... wide range of algorithms on phylogenetic trees, there exist only a few applications to work ... networks by computing distances between them or aligning them. Results: In order to improve this...
  • RAxML

  • Referenced in 40 articles [sw07716]
  • RAxML to infer a 10.000-taxon phylogenetic tree containing representative organisms from the three domains ... RAxML and PHYML on 8 synthetic alignments comprising 4.000 sequences...
  • STAMP

  • Referenced in 6 articles [sw17264]
  • also automatically builds multiple alignments, familial binding profiles and similarity trees when more than ... motif collection. STAMP is a highly flexible alignment platform, allowing users to ‘mix-and-match ... global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs may be inputted ... commonly used formats), consensus sequences, or alignments of known binding sites. STAMP also directly accepts...
  • SATCHMO-JS

  • Referenced in 2 articles [sw38908]
  • simultaneous protein multiple sequence alignment and phylogenetic tree construction ... present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO ... estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input ... higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus...
  • Statalign

  • Referenced in 5 articles [sw16609]
  • joint Bayesian estimation of alignments and evolutionary trees. Motivation: Bayesian analysis ... commonly used methods fix a single multiple alignment and consider only substitutions as phylogenetically informative...
  • DACTAL

  • Referenced in 2 articles [sw29613]
  • DACTAL: divide-and-conquer trees (almost) without alignments. Motivation: While phylogenetic analyses of datasets containing ... produces trees from unaligned sequence datasets without ever needing to estimate an alignment ... that each iteration begins with a tree produced in the prior iteration, decomposes the taxon ... SATé and maximum likelihood trees on estimated alignments using simulated and real datasets with...
  • BayesCAT

  • Referenced in 1 article [sw29694]
  • BayesCAT: Bayesian co-estimation of alignment and tree. Traditionally, phylogeny and sequence alignment are estimated ... distribution of a phylogenetic tree and a multiple sequence alignment. Our approach has a tree ... alternative previous approaches have a tree and an alignment. A large state space containing ... named BayesCAT (Bayesian Co-estimation of Alignment and Tree) is available at url{https://github.com...
  • SEPP

  • Referenced in 1 article [sw38914]
  • query sequences) into an existing phylogenetic tree and alignment on full-length sequences ... that alignment is used to find the optimal location in the phylogenetic tree ... input contains a highly accurate alignment and tree for the full-length sequences ... conquer technique to co-estimate alignments and trees on large molecular sequence datasets. We show...
  • AABB

  • Referenced in 4 articles [sw32949]
  • distance computation: The AABB (axis-aligned bounding box) tree component offers a static data structure...
  • Darwin

  • Referenced in 1 article [sw35912]
  • biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded...
  • MEGA4

  • Referenced in 7 articles [sw07695]
  • alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses...
  • PHAT

  • Referenced in 3 articles [sw17270]
  • improve the accuracy of sequence alignments and evolutionary trees of membrane proteins. Availability: http://www.blocks.fhcrc.org...