MEGA Version |
1.0 |
2.x |
3.x |
4.x |
Platform |
DOS |
Win |
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Win |
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Input Data | ||||
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DNA, Protein, Pairwise distance matrix |
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Sequence Alignment Construction | ||||
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Alignment Editor | ||||
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Manual editing of DNA and Protein sequences |
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Motif searching/highlighting |
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Synchronous alignment editing of original and translated cDNA |
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Copy/Paste sequences To/From Clipboard |
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Save alignment session for future display |
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Ability to read sequencer, MEGA, NEXUS, FASTA, and other formats |
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Apply color/highlight schemes to sequence data |
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Write alignment to MEGA file for direct analysis in MEGA |
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BLAST sequences from alignment directly |
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Multiple Sequence Alignment | ||||
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Complete native implementation of ClustalW |
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Ability to select all options on the fly |
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Ability to align any user-selected region |
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Ability to align translated cDNA sequences and automatic adjustment |
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Sequencer (Trace) File editor/viewer | ||||
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View ABI (*.abi, .ab1) and Studfen (*.std?) |
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Edit trace file |
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Mask vector (or any other region) |
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Launch direct BLAST search for whole or selected sequence |
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Send data directly to Alignment Editor |
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Integrated Web Browser and Sequence Fetching | ||||
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Direct "usual" web and GenBank browsing from MEGA |
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One-click sequence fetching from databanks queries |
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Send sequence data from BLAST search directly into alignment |
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Bookmark favorite sequence databank sites |
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Data Handling | ||||
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Handling ambiguous states (R,Y,T, etc.) |
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Extended MEGA format to save all data attributes |
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Importing Data from other formats (Clustal/Nexus/etc.) |
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Data Explorers | ||||
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Sequence |
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Distance matrix |
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Attributes supported | ||||
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Groups of Sequences/Taxa |
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Domains |
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Genes and Mixed Domain attributes |
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Explicit labels for sites |
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Automatic codon translation |
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Selection of codon positions |
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Selection of different site categories |
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Visual Specification of Domains/Groups |
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Center Analysis Preferences Dialog |
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Unlimited Data size for Analysis |
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Genetic Code Table Selection | ||||
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Choose a desired table |
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Ability to add/edit user defined tables |
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Computation of statistical attributes of a code table | ||||
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Degeneracy of codon positions |
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Numbers of potential synonymous sites |
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Inclusion of all known code tables |
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Real-Time Caption Expert Engine | ||||
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Generate Captions for Distance Matrices |
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Generate Captions for Phylogenies |
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Generate Captions for Tests |
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Generate Captions for Alignments |
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Copy Captions to External Programs |
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Save/Print Captions |
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Integrated Text File Editor | ||||
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Unlimited Text File Size |
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Multi-file Tabbed Display |
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Columnar Block selection/Editing |
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Undo/Redo operations |
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Line numbers |
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Utilities to Format Sequences/Reverse complement etc. |
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Copy Screenshots to EMF/WMF/Bitmap for presentation |
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Sequence Data Viewer | ||||
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Two dimensional display of molecular sequences |
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Display with identity symbol |
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Drag-drop sorting of sequences |
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Mixing coding and non-coding sequence display |
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One-click translation |
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Display with all or only selected taxa |
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Data Export | ||||
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PAUP3, PHYLIP |
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PAUP4, PHYLIP Interleaved |
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Highlighting | ||||
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0,2,4-fold degenerate sites |
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Variable, parsimony informative sites |
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Constant Sites |
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Statistical Quantities estimation | ||||
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DNA and protein sequence compositions |
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Estimation by genes/domains/groups |
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Codon Usage |
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Estimation by genes/domains/groups |
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Use only highlighted sites |
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MCL-based Estimation of Nucleotide Substitution Patterns | ||||
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4x4 Rate Matrix |
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Transition/Transversion Rate Ratios (k1, k2) |
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Transition/Transversion Rate Bias (R) |
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Substitution Pattern Homogeneity Test | ||||
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Composition Distance |
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Disparity Index |
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Monte-Carlo Test |
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Distance Estimation Methods | ||||
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Nucleotide-by-Nucleotide | ||||
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Models | ||||
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No. of differences, p-distance, Jukes-Cantor, Kimura 2P |
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Tajima-Nei, Tamura 3-parameter, Tamura-Nei distance |
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LogDet (Tamura-Kumar) |
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Maximum Composite Likelihood |
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Subcomponents | ||||
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Transitions (ts), tranversions (tv), ts/tv ratio |
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Number of common sites |
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Account for rate variation among sites |
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Relaxation of the homogeneity assumption |
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Synonymous/Nonsynonymous (Codon-by-Codon) | ||||
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Models | ||||
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Nei-Gojobori (1986) method |
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Modified Nei-Gojobori method |
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Li-Wu-Lou, PBL, Kumar method |
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Subcomponents | ||||
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Synonymous (s), nonsynonymous (n) distances |
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Numbers of synonymous and nonsynonymous sites |
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Differences and ratios (s-n, n-s, s/n, n/s) |
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4-fold degenerate site distances |
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0-fold degenerate site distances |
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Number of 0-fold and 4-fold degenerate sites |
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Protein distance | ||||
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Number of differences, p-distance, Poisson |
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Dayhoff and JTT distances |
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Account for rate variation among sites |
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Relaxation of the homogeneity assumption |
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Distance Calculations | ||||
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Pairwise |
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Between Group Average |
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Within Group Average |
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Net between group Average |
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Overall average |
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Sequence Diversity Calculations | ||||
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Mean Diversity within Subpopulations |
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Mean Diversity for Entire Population |
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Mean Interpopulational Diversity |
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Coefficient of Differentiation |
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Variance Calculations | ||||
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Analytical |
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Bootstrap |
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Handling missing data |
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Automatic translation |
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Automatic pasting of partial codons between exons |
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Tests of Selection | ||||
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Codon-based tests | ||||
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Large sample Z-test |
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Between Sequences |
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Within groups |
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Overall sequences |
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Fisher's Exact Test |
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Tajima's Test of Neutrality |
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Molecular Clock Test | ||||
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Tajima's relative rate test |
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Tree-making Methods | ||||
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Neighbor-Joining |
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Randomized tie-breaking in bootstrapping |
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Minimum Evolution method |
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Branch-swapping (Close-Neighbor-Interchange; CNI) |
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Fast OLS computation method |
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UPGMA |
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Randomized tie-breaking in bootstrapping |
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Maximum Parsimony | ||||
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Nucleotide sequences |
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Protein sequences |
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Max-mini branch-and-bound and min-mini searches |
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Branch-swapping (CNI) |
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Average branch length estimation |
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Bootstrap Test of Phylogeny | ||||
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Neighbor-joining/UPGMA |
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Minimum Evolution |
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Maximum Parsimony |
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Confidence Probability Test | ||||
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Neighbor-joining |
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Minimum Evolution |
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Consensus tree construction |
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Condensed tree construction |
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Distance Matrix Viewer | ||||
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View pairwise distances |
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View between group distances |
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View within group distances |
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View distances and standard errors simultaneously |
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Sort the distance matrix |
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Drag-and-drop |
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Group-wise |
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By Sequence names |
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Control display precision |
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Export Data for printing or re-importing |
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Tree Explorers | ||||
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Phylogeny Display and Graphic printing |
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On-the-spot taxa name editing |
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Multiple phylogeny views |
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Linearized Tree |
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Estimation of divergence time by calibrating molecular clock |
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Copy to Clipboard/save to file as an EMF drawing |
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Save to Newick format |
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Read trees from Newick format |
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User specified control for | ||||
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Placement and precision of branch length |
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Scale bar addition |
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Collapsing branches or groups |
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Display only a subtree |
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Ability to view multiple trees in different viewers |
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Tree Editing | ||||
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Flipping, re-rooting |
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Add marker symbols to names |
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Multi-color display and printing |
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Change Tree Size | ||||
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Vertical separation between taxa |
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Horizontal size |
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Change Tree shape |
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Multiple tree display |
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Save tree session for future display |
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What you see is what you get printing |
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Multi- or single page printing |
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Display images on tree for groups and taxa |
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