aprasad's tools [70 articles] Export

Recent papers added to aprasad's library classified by the tag tools. You can also see everyone's tools.

	TreeDyn: towards dynamic graphics and annotations for analyses of trees [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (10 October 2006), 439. by Francois Chevenet, Christine Brun, Anne L. Banuls, Bernard Jacq, Richard Christen posted to tree_visualization tools by aprasad on 2009-11-10 02:14:44 as along with 3 people foxpowa calderonv gjuggler
	BLAT--the BLAST-like alignment tool. [My Copy] Genome research, Vol. 12, No. 4. (1 April 2002), pp. 656-664. by James J. Kent posted to tools software alignment by aprasad on 2009-09-30 21:52:48 as along with 37 people and 3 groups azazello rshe dchughes rdowell gwallau druvus maria_hauser n00c sficklin Thaverkamp cpwardell daveGerrard coela daforerog pwais umit mmartin paszkows operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz yoanjacquemin talponer bozdagd gpappas LabDros BergmanLab EisenLab
	Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 13, No. 3. (June 1997), pp. 235-238. by A. Rambaut, N. C. Grassly posted to tools simulation seq-gen methods evolution by aprasad on 2009-08-25 00:02:13 as
	trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 15. (1 August 2009), pp. 1972-1973. by Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón posted to alignment alignment_error methods phylogenetics tools by aprasad on 2009-08-10 15:09:34 as along with 3 people and 1 group gjuggler ollieredfernwork nuin Orengo Group Journal Picks
	Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0 [My Copy] Mol Biol Evol, Vol. 26, No. 11. (1 November 2009), pp. 2581-2593. by Cory L. Strope, Kevin Abel, Stephen D. Scott, Etsuko N. Moriyama posted to evolution indel methods simulation tools by aprasad on 2009-08-09 13:25:49 as
	CpG Island Mapping by Epigenome Prediction [My Copy] PLoS Comput Biol, Vol. 3, No. 6. (8 June 2007), e110. by Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer posted to correlations epigraph genomics tools by aprasad on 2009-07-31 21:46:03 as along with 11 people hagechouchin443 iris42 suizifish bpcusack kaarsinogen sebastien_vigneau zwang oelemento fpattyn rschulz inesdesantiago
	CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure [My Copy] PLoS Genet, Vol. 2, No. 3. (3 March 2006), e26. by Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, Jörn Walter posted to correlations epigraph genomics tools by aprasad on 2009-07-31 21:45:02 as along with 9 people suizifish misonneh huiminC kaarsinogen eckart_bindewald olympos epigenetics oelemento clearbluespring
	JBrowse: A next-generation genome browser [My Copy] Genome Research, Vol. 19, No. 9. (1 September 2009), pp. 1630-1638. by Mitchell E. Skinner, Andrew V. Uzilov, Lincoln D. Stein, Christopher J. Mungall, Ian H. Holmes posted to browser genomics tools by aprasad on 2009-07-21 03:39:40 as along with 28 people and 2 groups hzoltan darian mkiyer daforerog n00c torfinnnome fenghezi djkt WXuan Zephyrus idonaldson pkonings inesdesantiago jcbarret jamselem urgi polivares cassj guhjy giovanni druvus natstreet fpattyn cisevol danmaclean timhubbard operon neils BergmanLab Journal picks
	OrthoSelect: a protocol for selecting orthologous groups in phylogenomics [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (16 July 2009), 219. by Fabian Schreiber, Kerstin Pick, Dirk Erpenbeck, Gert Worheide, Burkhard Morgenstern posted to est ortholog phylogenomics tools whole_genome by aprasad on 2009-07-20 16:36:56 as along with 7 people operon nuin Keywan GustavoLacerda zarskyv natstreet druvus
	rtracklayer: an R package for interfacing with genome browsers. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1841-1842. by Michael Lawrence, Robert Gentleman, Vincent Carey posted to bioinformatics r tools ucsc by aprasad on 2009-07-06 12:31:46 as along with 16 people and 3 groups daveGerrard iris42 guhjy dswan cisevol shikin inesdesantiago daforerog ppgardne natstreet nuin brianb kshameer neils chrisamiller druvus Bioinformatics BergmanLab Journal picks
	HMMoC a compiler for hidden Markov models [My Copy] Bioinformatics, Vol. 23, No. 18. (15 September 2007), pp. 2485-2487. by Gerton Lunter posted to algorithm hmm tools by aprasad on 2009-06-30 22:40:07 as along with 10 people druvus treangen alexeid guhjy operon AaronDarling rdiaz niallhaslam carlescorbi Alfie
	STEM: species tree estimation using maximum likelihood for gene trees under coalescence [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 971-973. by Laura S. Kubatko, Bryan C. Carstens, Lacey L. Knowles posted to congruence gene_geneology likelihood methods phylogenetics tools by aprasad on 2009-06-27 01:51:28 as along with 4 people lizbiogen nuin druvus djkt
	SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference [My Copy] Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 1274-1275. by D. Paraskevis, K. Deforche, P. Lemey, G. Magiorkinis, A. Hatzakis, A. M. Vandamme posted to bayesian congruence_landscapes methods phylogenetics tools by aprasad on 2009-06-26 17:27:31 as
	Swift: primary data analysis for the Illumina Solexa sequencing platform [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2194-2199. by Nava Whiteford, Tom Skelly, Christina Curtis, et al.Matt E. Ritchie, Andrea Lohr, Alexander W. Zaranek, Irina Abnizova, Clive Brown posted to illumina sequencing software tools by aprasad on 2009-06-25 22:00:11 as along with 21 people and 4 groups heliopais hzoltan dakelley sotacam lh49 djkt rtogawa cassj dswan torfinnnome rschulz natstreet druvus jasontsai jmeppley ghattem nuin polivares n00c niallhaslam idoerg Bioinformatics BergmanLab SIMR bioinformatics Journal picks
	Circos: An information aesthetic for comparative genomics [My Copy] Genome Research, Vol. 19, No. 9. (18 September 2009), pp. 1639-1645. by Martin Krzywinski, Jacqueline Schein, Ä°nanã§ Birol, et al.Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, Marco A. Marra posted to comparative_genomics tools visualization by aprasad on 2009-06-25 21:57:55 as along with 10 people and 1 group jmanning2k djkt rdiaz pkonings natstreet chrisamiller cisevol nuin idonaldson kshameer BergmanLab
	Simultaneous phylogeny reconstruction and multiple sequence alignment [My Copy] BMC Bioinformatics, Vol. 10, No. Suppl 1. (2009), S11. by Feng Yue, Jian Shi, Jijun Tang posted to alignment phylogenetics simultaneous_inference tools by aprasad on 2009-06-24 22:07:55 as along with 1 person cmzmasek
	Fast Statistical Alignment [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000392. by Robert K. Bradley, Adam Roberts, Michael Smoot, et al.Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter posted to alignment methods tools by aprasad on 2009-06-24 16:25:39 as along with 18 people and 1 group seb1 rdowell timflutre natstreet n00c yylin Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman djkt druvus Journal picks
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, Randal C. Linder, Tandy Warnow posted to alignment joint methods phylogenetics tools by aprasad on 2009-06-22 21:56:14 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings ppgardne dokky timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference [My Copy] Bioinformatics, Vol. 20, No. 3. (12 February 2004), pp. 407-415. by Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist posted to bayesian mrbayes phylogenetics tools by aprasad on 2009-06-15 21:47:55 as along with 1 person rvosa
	MrBayes 3: Bayesian phylogenetic inference under mixed models [My Copy] Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1572-1574. by F. Ronquist, J. P. Huelsenbeck posted to bayesian mrbayes phylogenetics tools by aprasad on 2009-06-15 21:45:47 as along with 7 people and 2 groups gwallau renewang alexeid chrn rvosa spavey AaronDarling LabDros FAB-lab
	Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology [My Copy] Science, Vol. 294, No. 5550. (14 December 2001), pp. 2310-2314. by John P. Huelsenbeck, Fredrik Ronquist, Rasmus Nielsen, Jonathan P. Bollback posted to bayesian methods mrbayes phylogenetics tools by aprasad on 2009-06-15 21:42:38 as along with 9 people and 1 group operon nuin seanyuan madhurjyag renewang bourscheid eustatic tny spavey FAB-lab
	AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 581-583. by Johan A. Nylander, James C. Wilgenbusch, Dan L. Warren, David L. Swofford posted to bayesian phylogenetics tools by aprasad on 2009-05-07 20:53:24 as along with 2 people and 1 group stajich mailund Mycology
	The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny [My Copy] (01 September 2003) edited by Marco Salemi, Anne-Mieke Vandamme posted to book phylogenetics tools by aprasad on 2009-04-23 22:00:33 as along with 1 person nuttpo
	Integrating sequence with FPC fingerprint maps [My Copy] Nucl. Acids Res. (30 January 2009), gkp034. by William Nelson, Carol Soderlund posted to fpc map tools by aprasad on 2009-03-18 17:18:19 as along with 1 person orzenil
	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2688-2690. by Stamatakis, Alexandros posted to likelihood phylogenetics raxml tools by aprasad on 2009-03-05 22:48:16 as along with 7 people hryk operon jpsullivan anisbet druvus johanviklund dmp
	MODELTEST: testing the model of DNA substitution [My Copy] Bioinformatics, Vol. 14, No. 9. (1 October 1998), pp. 817-818. by D. Posada, Ka Crandall posted to likelihood model_selection modeltest tools by aprasad on 2009-03-05 22:24:53 as along with 3 people lmichan eustatic jjhunt
	The UCSC Table Browser data retrieval tool. [My Copy] Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004) by D. Karolchik, A. S. Hinrichs, T. S. Furey, et al.K. M. Roskin, C. W. Sugnet, D. Haussler, W. J. Kent posted to tools ucsc by aprasad on 2009-03-05 22:09:32 as along with 4 people farhat miguel olympos heliopais
	The Jalview Java alignment editor. [My Copy] Bioinformatics, Vol. 20, No. 3. (12 February 2004), pp. 426-427. by M. Clamp, J. Cuff, S. M. Searle, G. J. Barton posted to alignment jalview tools by aprasad on 2009-03-05 22:08:15 as along with 3 people and 2 groups jwm CharlesM kcrawlik Radiation_Damage Stressosome
	Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006) by Rahul Siddharthan posted to alignment msa non-coding tools by aprasad on 2009-01-06 20:06:33 as along with 3 people and 2 groups cisevol dpollard lilou cis-regulatory-evolution EisenLab
	A Rapid Bootstrap Algorithm for the RAxML Web Servers [My Copy] Syst Biol, Vol. 57, No. 5. (1 October 2008), pp. 758-771. by Stamatakis, Alexandros, Hoover, Paul, Rougemont, Jacques posted to likelihood phylogenetics raxml tools by aprasad on 2008-10-23 04:28:27 as along with 2 people sim82 druvus
	REJECTOR: Software for Population History Inference from Genetic Data via a Rejection Algorithm [My Copy] Bioinformatics (20 October 2008), btn540. by Matthew J. Jobin, Joanna L. Mountain posted to coalescent demography method population_genetics simulation tools by aprasad on 2008-10-22 17:14:16 as along with 2 people druvus djkt
	Tools for simulating evolution of aligned genomic regions with integrated parameter estimation [My Copy] Genome Biology, Vol. 9, No. 10. (08 October 2008), R147. by Avinash Varadarajan, Robert K. Bradley, Ian H. Holmes posted to alignment evolution sequence simulation tools by aprasad on 2008-10-14 17:51:48 as along with 9 people inquil mhamada markusd nuin djkt treangen gjuggler pengchy druvus
	Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies [My Copy] Systematic Biology, Vol. 57, No. 5. (2008), pp. 785-794. by Tom M. Nye posted to phylogenetics tools tree_comparison tree_visualization by aprasad on 2008-10-13 18:26:30 as
	F-Seq: a feature density estimator for high-throughput sequence tags [My Copy] Bioinformatics, Vol. 24, No. 21. (1 September 2008), pp. 2537-2538. by Alan P. P. Boyle, Justin Guinney, Gregory E. E. Crawford, Terrence S. S. Furey posted to bed sequence tag tools by aprasad on 2008-09-15 02:37:16 as along with 18 people and 2 groups hzoltan n00c darian idonaldson michaelbarton inesdesantiago gdb ewilban1 tonamswish guhjy kmdaily cassj fhalbrit jfr rschulz polivares cthachuk zhouyu JLab BergmanLab
	Segment-based multiple sequence alignment [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192. by Tobias Rausch, Anne K. Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert posted to alignment methods msa tools by aprasad on 2008-08-13 18:59:33 as along with 9 people nuin BioNica darian Md_2007 zwang Ema APRegier djkt groepl
	NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences. [My Copy] Genomics (27 May 2008) by Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. F. Stadler, Jörg Hackermüller posted to alignment methods msa tools by aprasad on 2008-07-30 16:16:50 as along with 1 person maximilianh
	jModelTest: Phylogenetic Model Averaging [My Copy] Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1253-1256. by David Posada posted to methods model_choice tools by aprasad on 2008-06-26 21:29:49 as along with 4 people Garamonfok BioNica operon druvus
	primetv: A viewer for reconciled trees [My Copy] BMC Bioinformatics, Vol. 8 (07 May 2007), 148. by Bengt Sennblad, Eva Schreil, Ann, Jens Lagergren, Lars Arvestad posted to methods tools tree_visualization by aprasad on 2008-06-19 22:45:22 as along with 2 people druvus gendlerk
	Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences. [My Copy] Syst Biol, Vol. 56, No. 6. (December 2007), pp. 988-1010. by D. A. Morrison posted to likelihood methods phylogenetics tools by aprasad on 2008-03-29 08:24:22 as along with 2 people druvus akifumi
	Uncertainty in homology inferences: assessing and improving genomic sequence alignment. [My Copy] Genome research, Vol. 18, No. 2. (1 February 2008), pp. 298-309. by Gerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, Jotun Hein posted to alignment methods tools by aprasad on 2008-02-07 18:56:32 as along with 8 people brant treangen djkt grahamc dandaman mailund gjuggler AaronDarling
	A novel algorithm and web-based tool for comparing two alternative phylogenetic trees [My Copy] Bioinformatics, Vol. 22, No. 1. (1 January 2006), pp. 117-119. by Tom M. Nye, Pietro Lio, Walter R. Gilks posted to tools tree_comparison tree_visualization by aprasad on 2008-02-06 23:19:37 as along with 3 people druvus dparks blindAngle
	Paloverde: an OpenGL 3-D phylogeny browser. [My Copy] Bioinformatics (24 February 2006) by Michael J. J. Sanderson posted to phylogenetics tools tree_visualization by aprasad on 2008-02-06 22:52:01 as along with 4 people AaronDarling dparks eckart_bindewald akifumi
	Analysis and Visualization of Tree Space [My Copy] Syst Biol, Vol. 54, No. 3. (1 June 2005), pp. 471-482. by David Hillis, Tracy Heath, Katherine John posted to phylogenetics tools tree_visualization by aprasad on 2008-02-06 22:49:40 as
	OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics [My Copy] BMC Evolutionary Biology, Vol. 7, No. 1. (30 November 2007), 241. by Vincent Ranwez, Frederic Delsuc, Sylvie Ranwez, Khalid Belkir, Marie K. Tilak, Emmanuel J. P. Douzery posted to database mammalian phylogenetics tools by aprasad on 2008-01-25 16:10:13 as along with 4 people and 1 group avilella gjuggler bpcusack idonaldson Ensembl Compara citations
	RadCon: phylogenetic tree comparison and consensus [My Copy] Bioinformatics, Vol. 16, No. 5. (1 May 2000), pp. 486-487. by Joseph L. Thorley, Roderic D. Page posted to consensus phylogenetics tools tree by aprasad on 2008-01-16 20:37:13 as along with 2 people tny sterovetta
	Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference. [My Copy] Nat Protoc, Vol. 2, No. 11. (2007), pp. 3022-3030. by W. J. Murphy, S. J. O'Brien posted to comparative_genomics map methods primer tools by aprasad on 2007-11-26 15:09:24 as
	INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events. [My Copy] Nucleic Acids Res (21 May 2007) by Feng, Chueng, Trees posted to indel methods tools by aprasad on 2007-09-13 22:20:10 as along with 5 people and 1 group natstreet druvus guhjy dpollard lilou EisenLab
	DNA assembly with gaps (Dawg): simulating sequence evolution. [My Copy] Bioinformatics, Vol. 21 Suppl 3 (1 November 2005) by R. A. Cartwright posted to evolution phylogenetics sequence simulation tools by aprasad on 2007-09-10 15:50:05 as along with 2 people timflutre gjuggler
	Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment [My Copy] Bioinformatics, Vol. 23, No. 3. (1 February 2007), pp. 289-297. by Jaebum Kim, Saurabh Sinha posted to alignment indel tools by aprasad on 2007-09-02 13:38:06 as along with 4 people and 1 group timflutre gjuggler druvus indigoviolet EisenLab
	CONSEL: for assessing the confidence of phylogenetic tree selection. [My Copy] Bioinformatics, Vol. 17, No. 12. (December 2001), pp. 1246-1247. by H. Shimodaira, M. Hasegawa posted to consel likelihood methods tools by aprasad on 2007-08-31 21:55:04 as along with 2 people druvus polpotak

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phylogenetics	249
tree	119
evolution	109
methods	107
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mammal	71
review	71
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indel	51
repeats	47
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cns	31
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genomics	26
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targeted_sequencing	1
taxon_sampling	1
tetraodon	1
textbook	1
thomas	1
transcription	1
trees	1
tree_shrew	1
trophoblast	1
tuatara	1
upgma	1
uprobe	1
usage	1
visualization	1
web	1
wgs	1
whale	1
xenarthra	1

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