TNT: Tree Analysis Using New Technology

  title={TNT: Tree Analysis Using New Technology},
  author={Gonzalo Giribet},
  journal={Systematic Biology},

Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life

It is determined that conserved codon pairing typically has a smaller window size than the length of a ribosome, andCodon pairing tracks phylogenies across various taxonomic groups and should be considered in conjunction with other phylogenomic techniques.

SDM : A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics

This work proposes a novel method, named super distance matrix (SDM), which follows the same line as average consensus supertree (ACS) and combines the evolutionary distances obtained from each gene into a single distance supermatrix to be analyzed using a standard distance-based algorithm.

Cladistic analysis of some taxa in Malvaceae s.l. “Core Malvales” based on anatomical characteristics -

The results of the phylogenetic analysis conducted from the cladogram (rooted tree) based on 44 anatomical characters and 111 character states strongly support the monophyly of family Malvaceae s.l. while, the other three families are para- or polyphyletic.

Phylogeny and higher classification of Mutillidae (Hymenoptera) based on morphological reanalyses

This study aimed to resolve the differences in the two currently used classifications of Mutillidae, and proposes the recognition of eight subfamilies, with Notably, Myrmosinae were consistently strongly supported as monophyletic with the remainingMutillidae (disagreeing with a recent molecular analysis), and thus retained as a mutillid subfamily.

A new catostomid fish (Ostariophysi, Cypriniformes) from the Eocene Kishenehn Formation and remarks on the North American species of †Amyzon Cope, 1872

A new catostomid species of the genus †Amyzon Cope, 1872 from the Eocene Kishenehn Formation in Montana, USA is described, and phylogenetic analyses suggest that the new species is the sister group of †A.

On the phylogeny and evolution of Mesozoic and extant lineages of Adephaga (Coleoptera, Insecta)

The relationships of extant and extinct lineages of Adephaga were analysed formally for the first time and possible reasons for the extinction of †Coptoclavidae are the rise of teleost fish and the competition of Gyrinidae and Dytiscidae, which possess efficient defensive glands and larval mandibular sucking channels.

Systematics of Leptomorphus and phylogeny of the Sciophilini (Diptera: Mycetophilidae)

A taxonomic revision and phylogenetic analysis of the world fauna of Leptomorphus Curtis were undertaken and 10 new generic combinations resulted from recognition of the new genus Duretophragma.

Systematics: A Course of Lectures

A molecular phylogeny of annelids

Parsimony analyses of annelids based on the largest taxon sample and most extensive molecular data set yet assembled suggest that the poor resolution in the basal parts of the trees presented here may be due to lack of signal connected to incomplete data sets, rapid radiation events and/or uneven evolutionary rates and long‐branch attraction.



Techniques for Analyzing Large Data Sets

The techniques described here have so far been used only for prealigned sequences, but they could be adapted for other methods of analysis, like the direct optimization method of Wheeler.

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

With the ratchet, Goloboff's NONA, and existing computer hardware, data sets that were previously intractable or required months or years of analysis with PAUP* can now be adequately analyzed in a few hours or days.


  • P. Goloboff
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1993
Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non‐iterative and does not require independent estimations of weights. It is based on searching

Methods for Quick Consensus Estimation

A way to collapse branches considering suboptimal trees is described, which can be extended as a measure of relative support for groups; the relative support is based on the Bremer support, but takes into account relative amounts of favorable and contradictory evidence.

Improvements to resampling measures of group support

Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies

Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima

New methods for parsimony analysis of large data sets are presented, including sectorial searches, tree‐drifting, and tree‐fusing which find a shortest tree in less than 10 min and perform well in other cases analyzed.


A phylogenetic analysis of the genera of Cyphophthalmi is undertaken by studying 32 morphological characters in 43 species representing all families and most genera, and molecular characters strongly support the monophyly of Troglosironidae + Neogoveidae.

NEXUS: an extensible file format for systematic information.

The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program.


  • K. Bremer
  • Biology
    Evolution; international journal of organic evolution
  • 1988
Cladistic analysis of amino acid sequence data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated.


  • J. Felsenstein
  • Economics
    Evolution; international journal of organic evolution
  • 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.