Good Phylogenetic Tree Display Program

Archaeopteryx. This is my favorite. It is responsive given large trees and is one of the few supporting topology editing. Nonetheless, the circular view, which is in alpha, is not as good as others. I do not like its black background, either.
FigTree. A nice tree viewer. Work efficiently with medium to large trees. It is more versatile than Archaeopteryx on viewing (e.g. the fish-eye mode and the circular layout). No topology editing.
Dendroscope. A viewer (almost no editing options) designed for huge trees. The selling point is its efficiency, better than both FigTree and Archaeopteryx. Nonetheless, it does not seem to aim to produce publication-ready figures (e.g. no subtree highlighting). The circular view, like in Archaeopteryx, looks ugly because texts are not rotated.
Jstree. My hobby. The first Javascript based tree editor, supporting operations such as subtree cut-and-paste. In firefox/opera/chrome/safari, it is pretty responsive for medium to large trees.
PhyloWidget. It has a very impressive user interface, smooth and responsive given large trees. It supports topology editing. My major complaints are: a) I frequently scroll the tree out of the canvas but do not know how to get it back quickly; b) at least on my laptop, it is eating up CPU without actually doing anything.
iTOL. A very nice tree viewer (no editing) written in Flash, but the responsiveness is not as good as those Java-based viewers. For medium trees, its rectangle view only displays the first tens of leaves.
TreeGraph2. As is stated in its paper, treegraph2 mainly aim to produce beautiful high-quality figures for small trees. It supports many operations on trees, but its responsiveness is very bad.
Mesquite. A very comprehensive software suite. It is efficient enough for large trees, but the user interface is not very friendly.
TreeDyn. I have heard a lot of good things about it, but unfortunately, its Mac binary is not working in Mac OS X 10.6, so I have not tried.
TreeViewJ. Nice UI, but not efficient enough for medium trees.
Treevoletion. Nice UI, but inefficient for medium trees.

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How to keep chain ID / IDs in GROMACS?

In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]

Python : Turtle tree

Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========...

How to use MODELLER to build DIMER homology model with ligand?

How to use MODELLER to build DIMER homology model with ligand? Procedure: Get Fasta sequence from UNIPROT database. Predict sequence alignment from HHPRED Prepare INPUT files for MODELLER model-dimer.py (Click to download) ############### from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = environ() env.io.hetatm = True a = automodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, ...

Plagarism Checker

Plagiarism is a serious academic misconduct. Whether you are a student writing a college essay, a teacher reviewing a student’s submission, or just someone who works extensively with content, it is important to ensure that the content is not plagiarized. Following are some resources to check Plagiarism. http://www.plagscan.com https://www.plagramme.com/ http://www.plagiarisma.net/fr/# http://www.scanmyessay.com http://www.plagtracker.com http://www.duplichecker.com http://www.smallseotools.com/plagiarism-checker http://www.plagium.com/fr/detecteurdeplagiat http://www.paperrater.com/plagiarism_checker http://www.copyleaks.com http://www.plagiarismchecker.com http://www.quetext.com http://plagiarismdetector.net http://www.solidseotools.com/plagiarism-checker http://www.dustball.com/cs/plagiarism.checker http://www.articlechecker.com http://www.plagiarismcheck.org

Homology model validation

Homology model can be validated in multiple ways. Here you will find useful description on how to validate your homology model. Web-servers: UCLA-DOE LAB — SAVES : The Structure Analysis and Verification Server ( New Link ) This metaserver runs 6 programs for checking and validating protein structures during and after model refinement. PROCHECK : Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. WHAT_CHECK : Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model. ERRAT : Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures. VERIFY_3D : Determines the ...

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