Address of the bookmark: https://chunlab.wordpress.com/tetra-nucleotide-analysis/

Sequence Analysis and General Bioinformatics

• BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly
• Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly
• Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley & Sons
• Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley & Sons
• Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press
• Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall
• Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann
• Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press
• Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub
• Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings
• Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley & Sons
• Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press
• Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers
• Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley & Sons
• Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag
• Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience
• Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press
• Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall
• Bioinformatics: A Primer, Charles Staben, 2001, Jones & Bartlett Pub
• Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics
• Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press
• Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co
• Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press
• Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science
• Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley & Sons
• Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press
• Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press
• Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society
• Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press
• Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press
• Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press
• Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press
• Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers
• Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc.
• Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd.
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press
• Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press
• Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co.
• Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press
• Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press
• High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub.
• Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press
• DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press
• Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter
• Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman & Hall
• Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press
• Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press
• Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press
• Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society
• Mathematical Methods for DNA Sequences, Michael S. Waterman (Editor), 1989, CRC Press

Programming Books for Bioinformatics

• Mastering Perl for Bioinformatics, James D. Tisdall, 2003, O'Reilly
• Genomic Perl: From Bioinformatics Basics to Working Code, Rex A. Dwyer, 2002, Cambridge University Press
• Beginning Perl for Bioinformatics, James Tisdall, 2001, O'Reilly
• Developing Bioinformatics Computer Skills, Cynthia Gibas, Per Jambeck, 2001, O'Reilly

General Genomics

• Functional Microbial Genomics (Volume 33), Brendan Wren, Nick Dorrell, 2003, Academic Press
• Discovering Genomics, Proteomics, and Bioinformatics, A. Malcolm Campbell, Laurie J. Heyer, 2002, Benjamin/Cummings
• Genomes, Terence A. Brown, 2002, John Wiley & Sons
• Essentials of Medical Genomics, Stuart M. Brown , 2002, John Wiley & Sons
• A Primer of Genome Science, Greg Gibson, Spencer V. Muse, 2002, Sinauer Associates
• Pathogen Genomics: Impact on Human Health, Karen Joy, Phd Shaw (Editors), 2002, Humana Press
• Genomics, John E. Antonopoulos, 2000, Xlibris Corporation
• Genomics and Proteomics: Functional and Computational Aspects, Sandor Suhai (Editor), 2000, Plenum Pub Corp
• Functional Genomics: A Practical Approach (The Practical Approach Series, 235), S. Hunt and F. Livesey (Editors), 2000, Oxford Univ Press
• Human Molecular Genetics, Andrew P. Read, Tom Strachan 1999, BIOS Scientific Publishers Ltd.
• Genomics: The Science and Technology Behind the Human Genome Project, Charles R. Cantor and Cassandra L. Smith, 1999, John Wiley & Sons
• Cells: A Laboratory Manual, 3 volumes, David L. Spector, Robert D. Goldman, Leslie A. Leinwand, 1998, Cold Spring Harbor Laboratory Press
• Genome Analysis: A Laboratory Manual, 4 volumes, Bruce Birren, et al. (Editors), 1997, Cold Spring Harbor Laboratory Press
• The Human Genome Project, N. G. Cooper (Editor), 1994, University Science Books

Comparative Genomics

• Handbook of Comparative Genomics: Principles and Methodology, Cecilia Saccone, Graziano Pesole, 2003, Wiley-Liss
• Sequence - Evolution - Function: Computational Approaches in Comparative Genomics, Eugene V. Koonin, Michael Y. Galperin, 2002, Kluwer Academic Publishers
• Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, David Sankoff and Joseph H. Nadeau, 2000, Kluwer Academic Pub
• Comparative Genomics, Melody Clark (Editor), 2000, Kluwer Academic Pub

Proteomics

• Proteins and Proteomics: A Laboratory Manual, Richard J. Simpson (Editor), Cold Spring Harbor Laboratory
• Proteomics in Practice: A Laboratory Manual of Proteome Analysis , Reiner Westermeier, Tom Naven, 2002, John Wiley & Sons
• Posttranslational Modifications of Proteins: Tools for Functional Proteomics (Methods in Molecular Biology, Vol 194) , Christoph Kannicht (Editor), 2002, Humana Press
• Peptide Arrays on Membrane Supports: Synthesis and Applications (Springer Lab Manual), Joachim Koch, Michael Mahler (Editors), 2002, Springer Verlag
• Proteomics , Timothy Palzkill, 2002, Kluwer Academic Publishers
• Introduction to Proteomics: Tools for the New Biology , Daniel C. Liebler (Editor), 2001, Humana Press
• Proteome Research: Mass Spectrometry (Principles and Practice) , P. James (Editor), 2001, Springer Verlag
• Interpreting Protein Mass Spectra: A Comprehensive Resource , A. Peter Snyder, 2000, American Chemical Society
• Protein Sequencing and Identification Using Tandem Mass Spectrometry , Michael Kinter, Nicholas E. Sherman, 2000, Wiley-Interscience
• From Genome to Proteome: Advances in the Practice and Application of Proteomics, Michael J. Dunn (Editor), 2000, Vch Verlagsgesellschaft Mbh
• Proteomics: From Protein Sequence to Function, S. Pennington (Editor), M. Dunn (Editor), 2000, Springer Verlag
• Proteome Research: Two-Dimensional Gel Electrophoresis and Detection Methods (Principles and Practice), T. Rabilloud (Editor), 2000, Springer Verlag
• Proteome and Protein Analysis, R. M. Kamp, D. Kyriakidis, th Choli-Papadopoulou (Editor), 1999, Springer Verlag
• Proteome Research: New Frontiers in Functional Genomics, M. R. Wilkins, et al. (Editors), 1997, Springer Verlag

Protein Structure

• Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley & Sons
• Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line
• Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press
• Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press
• Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing
• Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht, 1999, Freeman

Pharmacogenomics

• Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Mark A. Rothstein (Editor), 2003, Wiley-Liss
• Pharmacogenomics: The Search for Individualized Therapies, Julio Licinio, Ma-Li Wong (Editors), 2002, John Wiley & Sons
• Pharmacogenomics, Werner Kalow, Urs A. Meyer, Rachel Tyndale (Editors), 2001, Marcel Dekker
• Pharmacogenetics and Pharmcogenomics: Recent Conceptual and Technical Advances (Pharmacology, Volume 61, Number 3, 2000), Elliot S. Vesell (Editor), 2000, S. Karger Publishing
• Pharmacogenetics, Wendell Weber, 1997, Oxford University Press

DNA Microarrays

• Statistical Analysis of Gene Expression Microarray Data, T. P. Speed (Editor), 2003, CRC Press
• Microarray Gene Expression Data Analysis: A Beginner's Guide, Helen C. Causton, John Quackenbush, Alvis Brazma, 2003, Blackwell Publishers
• The Analysis of Gene Expression Data (Statistics for Biology and Health), G. Parmigiani, E. S. Garrett, R. A. Irizarry, S. Zeger , Graeme Clark (Editors), 2003, Springer Verlag
• A Practical Approach to Microarray Data Analysis, Daniel P. Berrar, Werner Dubitzky, Martin Granzow (Editors), 2002, Kluwer Academic Publishers
• DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Pierre Baldi, G. Wesley Hatfield, 2002, Cambridge University Press
• DNA Microarrays: A Molecular Cloning Manual, David Bowtell, Joseph Sambrook (Editors), 2002, Cold Spring Harbor Laboratory
• DNA Array Image Analysis: Nuts & Bolts, Gerda Kamberova, Shishir Shah, 2002, DNA Press
• Microarray Analysis, Mark Schena, 2002, John Wiley & Sons
• A Biologist's Guide to Analysis of DNA Microarray Data, Steen Knudsen, 2002, John Wiley & Sons
• Microarrays for an Integrative Genomics (Computational Molecular Biology), Isaac S. Kohane, Alvin Kho, Atul J. Butte, 2002, MIT Press
• Microarrays for the Neurosciences: An Essential Guide (Cellular and Molecular Neuroscience), Daniel H. Geschwind, Jeffrey P. Gregg (Editors), 2002, MIT Press
• DNA Microarrays: Gene Expression Applications, Bertrand Jordan (Editor), 2001, Springer Verlag
• DNA Arrays: Methods and Protocols (Methods in Molecular Biology, Volume 170), Jang B. Rampal (Editor), 2001, Humana Press
• DNA Arrays: Technologies and Experimental Strategies, Elena V. Grigorenko (Editor), 2001, CRC Press
• Microarray Biochip Technology, Mark Schena (Editor), 2000, Eaton Pub
• Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series), Michael McClelland (Editor), Arthur B. Pardee (Editor), 1999, Eaton Pub
• DNA Microarrays: A Practical Approach (Practical Approach Series 205), Mark Schena (Editor), 1999, Oxford Univ Press
• cDNA Preparation and Characterization (Methods in Enzymology Volume 303), S.M. Weissman (Editor), 1999, Academic Press

Systems Biology, Genetic and Biochemical Network

• Handbook of Graphs and Networks : From the Genome to the Internet, Stefan Bornholdt, Heinz Georg Schuster (Editors), 2003, Vch Verlagsgesellschaft Mbh
• Computational Cell Biology, Christopher Fall, Eric Marland, John Wagner, John Tyson (Editors), 2002, Springer Verlag
• Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology), Julio Collado-Vides, Ralf Hofestadt (Editors), 2002, MIT Press
• Foundations of Systems Biology, Hiroaki Kitano (Editor), 2001, MIT Press
• Genomic Regulatory Systems: Development and Evolution, Eric H. Davidson , 2001, Academic Press
• Genes & Signals, Mark Ptashne, Alexander Gann, 2001, Cold Spring Harbor Laboratory
• Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), James M. Bower and Hamid Bolouri (Editors), 2001, MIT Press
• Protein-Protein Interactions: A Molecular Cloning Manual, Erica Golemis (Editor), 2001, Cold Spring Harbor Laboratory
• Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Eberhard O. Voit, 2000, Cambridge University Press
• Mathematical Physiology, James P. Keener, James Sneyd, 1998, Springer Verlag

DNA Sequencing

• DNA Sequencing: From Experimental Methods to Bioinformatics (Introduction to Biotechniques Series), Luke Alphey, 1997, Springer Verlag
• Automated DNA sequencing and analysis, Adams M.D., Fields C., Venter J.C. (Editors), 1994, Academic Press

Apart from above mentioned books, you can also find some useful books links at following mentioned URLs:

http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713

http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545

http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068

http://books.google.no/books?id=pxSM7R1sdeQC&dq=Pierre+baldi+%2B+bioinformatics&printsec=frontcover&source=bn&hl=en&ei=IoGRS6uCIJT-NYLA8Z0N&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q&f=false

http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826

If you think your favourite books are not listed then please write it down in comment section for the benefits of other users. Feel free to add many more books in comment section. 

Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates.

http://www.ibens.ens.fr/?rubrique43&lang=fr

Address of the bookmark: https://github.com/DyogenIBENS/LibsDyogen

Explore your trees directly in the browser, and annotate them with various types of data.

iTOL can easily visualize trees with 50'000 or more leaves. With advanced search capabilities and display of unrooted, circular and regular cladograms or phylograms, exploring and navigating trees of any size is simple.

https://itol.embl.de/

Address of the bookmark: https://itol.embl.de/

Description
This free online-only RevBayes workshop will provide an introduction to the theory and use of RevBayes, with a focus on (1) tree inference from molecular data, (2) analyses combining fossil and extant taxa, and (3) evaluating MCMC performance, with advanced topics including assessing model adequacy and macroevolutionary analyses. Additional topics may be added depending on the interests of selected participants. The format will be a combination of interactive video sessions (via Zoom or similar tools), real-time discussions over Slack, self-guided tutorials, and pre-recorded videos.

The initial session will resolve technical issues and present the basics of using RevBayes. Participants will then be expected to work through several tutorials on their own schedule, with the help of pre-recorded materials. A Slack forum will be open for questions and issues. The workshop will conclude with several online Q&A sessions with the instructors. The dates for the interactive sessions are currently tentative and may be adjusted depending on the schedules of the participants and instructors.

We are hoping to identify up to 15 participants for this online course. While we hope we are able to accommodate everyone who applies, we realize that this may not be possible because of time-zones and availability. If the number of applicants exceeds our capacity, we hope to organize a second round of sessions later in the year. Participants will not be charged for the course, but we will request that they commit to completing the tutorials and attending a majority of interactive sessions.

To apply to this course, please go to the registration form and submit your application by July 6, 2020.

More at https://revbayes.github.io/workshops/online2020.html

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

General information.

Field terminator is "\t|\t"

Row terminator is "\t|\n"

nodes.dmp file consists of taxonomy nodes. The description for each node includes the following

fields:

tax_id -- node id in GenBank taxonomy database

  parent tax_id -- parent node id in GenBank taxonomy database

  rank -- rank of this node (superkingdom, kingdom, ...) 

  embl code -- locus-name prefix; not unique

  division id -- see division.dmp file

  inherited div flag  (1 or 0) -- 1 if node inherits division from parent

  genetic code id -- see gencode.dmp file

  inherited GC  flag  (1 or 0) -- 1 if node inherits genetic code from parent

  mitochondrial genetic code id -- see gencode.dmp file

  inherited MGC flag  (1 or 0) -- 1 if node inherits mitochondrial gencode from parent

  GenBank hidden flag (1 or 0)            -- 1 if name is suppressed in GenBank entry lineage

  hidden subtree root flag (1 or 0)       -- 1 if this subtree has no sequence data yet

  comments -- free-text comments and citations

Taxonomy names file (names.dmp):

tax_id -- the id of node associated with this name

name_txt -- name itself

unique name -- the unique variant of this name if name not unique

name class -- (synonym, common name, ...)

Divisions file (division.dmp):

division id -- taxonomy database division id

division cde -- GenBank division code (three characters)

division name -- e.g. BCT, PLN, VRT, MAM, PRI...

comments

Genetic codes file (gencode.dmp):

genetic code id -- GenBank genetic code id

abbreviation -- genetic code name abbreviation

name -- genetic code name

cde -- translation table for this genetic code

starts -- start codons for this genetic code

Deleted nodes file (delnodes.dmp):

tax_id -- deleted node id

Merged nodes file (merged.dmp):

old_tax_id                              -- id of nodes which has been merged

new_tax_id                              -- id of nodes which is result of merging

Citations file (citations.dmp):

cit_id -- the unique id of citation

cit_key -- citation key

pubmed_id -- unique id in PubMed database (0 if not in PubMed)

medline_id -- unique id in MedLine database (0 if not in MedLine)

url -- URL associated with citation

text -- any text (usually article name and authors).

-- The following characters are escaped in this text by a backslash:

-- newline (appear as "\n"),

-- tab character ("\t"),

-- double quotes ('\"'),

-- backslash character ("\\").

taxid_list -- list of node ids separated by a single space

Part I – Basic Find Commands for Finding Files with Names
1. Find Files Using Name in Current Directory

Find all the files whose name is gene.txt in a current working directory.

# find . -name gene.txt

./gene.txt

2. Find Files Under Home Directory

Find all the files under /home directory with name gene.txt.

# find /home -name gene.txt

/home/gene.txt

3. Find Files Using Name and Ignoring Case

Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.

# find /home -iname gene.txt

./gene.txt
./Gene.txt

4. Find Directories Using Name

Find all directories whose name is Gene in / directory.

# find / -type d -name Gene

/Gene

5. Find fasta Files Using Name

Find all php files whose name is gene.fasta in a current working directory.

# find . -type f -name gene.fasta

./gene.fasta

6. Find all PHP Files in Directory

Find all fasta files in a directory.

# find . -type f -name "*.fasta"

./gene.fasta
./cancer.fasta
./allgene.fasta

Part II – Find Files Based on their Permissions
7. Find Files With 777 Permissions

Find all the files whose permissions are 777.

# find . -type f -perm 0777 -print

8. Find Files Without 777 Permissions

Find all the files without permission 777.

# find / -type f ! -perm 777

9. Find SGID Files with 644 Permissions

Find all the SGID bit files whose permissions set to 644.

# find / -perm 2644

10. Find Sticky Bit Files with 551 Permissions

Find all the Sticky Bit set files whose permission are 551.

# find / -perm 1551

11. Find SUID Files

Find all SUID set files.

# find / -perm /u=s

12. Find SGID Files

Find all SGID set files.

# find / -perm /g+s

13. Find Read Only Files

Find all Read Only files.

# find / -perm /u=r

14. Find Executable Files

Find all Executable files.

# find / -perm /a=x

15. Find Files with 777 Permissions and Chmod to 644

Find all 777 permission files and use chmod command to set permissions to 644.

# find / -type f -perm 0777 -print -exec chmod 644 {} \;

16. Find Directories with 777 Permissions and Chmod to 755

Find all 777 permission directories and use chmod command to set permissions to 755.

# find / -type d -perm 777 -print -exec chmod 755 {} \;

17. Find and remove single File

To find a single file called gene.txt and remove it.

# find . -type f -name "gene.txt" -exec rm -f {} \;

18. Find and remove Multiple File

To find and remove multiple files such as .fa or .gb, then use.

# find . -type f -name "*.fa" -exec rm -f {} \;

OR

# find . -type f -name "*.gb" -exec rm -f {} \;

19. Find all Empty Files

To file all empty files under certain path.

# find /tmp -type f -empty

20. Find all Empty Directories

To file all empty directories under certain path.

# find /tmp -type d -empty

21. File all Hidden Files

To find all hidden files, use below command.

# find /tmp -type f -name ".*"

Part III – Search Files Based On Owners and Groups
22. Find Single File Based on User

To find all or single file called gene.txt under / root directory of owner root.

# find / -user root -name gene.txt

23. Find all Files Based on User

To find all files that belongs to user Rahul under /home directory.

# find /home -user rahul

24. Find all Files Based on Group

To find all files that belongs to group Developer under /home directory.

# find /home -group developer

25. Find Particular Files of User

To find all .txt files of user Rahul under /home directory.

# find /home -user rahul -iname "*.txt"

Part IV – Find Files and Directories Based on Date and Time
26. Find Last 50 Days Modified Files

To find all the files which are modified 50 days back.

# find / -mtime 50

27. Find Last 50 Days Accessed Files

To find all the files which are accessed 50 days back.

# find / -atime 50

28. Find Last 50-100 Days Modified Files

To find all the files which are modified more than 50 days back and less than 100 days.

# find / -mtime +50 –mtime -100

29. Find Changed Files in Last 1 Hour

To find all the files which are changed in last 1 hour.

# find / -cmin -60

30. Find Modified Files in Last 1 Hour

To find all the files which are modified in last 1 hour.

# find / -mmin -60

31. Find Accessed Files in Last 1 Hour

To find all the files which are accessed in last 1 hour.

# find / -amin -60

Part V – Find Files and Directories Based on Size
32. Find 50MB Files

To find all 50MB files, use.

# find / -size 50M

33. Find Size between 50MB – 100MB

To find all the files which are greater than 50MB and less than 100MB.

# find / -size +50M -size -100M

34. Find and Delete 100MB Files

To find all 100MB files and delete them using one single command.

# find / -size +100M -exec rm -rf {} \;

35. Find Specific Files and Delete

Find all .gb files with more than 10MB and delete them using one single command.

# find / -type f -name *.gb -size +10M -exec rm {} \;

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. 
Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.
The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.

For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.

Phylogeny and Reconstructing Phylogenetic Trees: http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html
the CBRG and Department of Statistics Phylogeny tutorial: http://www.compbio.ox.ac.uk/tutorials/phylogeny/
TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html

PHYLIP: http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html
An Introduction to Molecular Phylogeny: http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf

How to make a phylogenetic tree: http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Treetutorial.html
Phylogenetic Trees: http://cnx.org/content/m11052/latest/
Phylogeny by Ron Shamir: http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf
Introduction to Phylogeny: http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm
Lecturer notes on Phylogeny: http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf
Principles and Practice of Phylogenetic Systematics:http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm

Inferring phylogenetic trees: http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf

Lecture Notes

Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:http://academic.emporia.edu/mooredwi/nathist/chap1.htm

Algorithms for Phylogenetic Reconstructions:http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf

Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail : http://www.phylogeny.fr/version2_cgi/index.cgi

A Brief Tutorial on Phylogenetics
http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf

A Brief Tutorial on Phylogenetics Human Rabbit Chicken
http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf

Phylogenetic Tree Computation Tutorial Overview
http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf

MrBayes: A program for the Bayesian inference of phylogeny
http://golab.unl.edu/teaching/SBseminar/manual.pdf

Web sites providing software for the construction of phylogenetic trees

• BioEdit

• Coelocanth-Fish Out of Time

• Computational Biochemistry Research Group

• Digital Taxonomy

• Hennig 86

• Hyperclean from Bioinformatics Solutions, Inc.

• Memorial University of Newfoundland

• Mr. Bayes

• NONA

• Oxford University Evolutionary Biology Group

• Paleobiology Database

• PAUP

• Phylip Homepage

• Poy

• Sinauer Associates

• TNT-Tree Analysis Using New Technology

• Tree Base

• Treefinder

• Tree-Puzzle

• Tree View-Taxonomy and Systematics Group at Glasgow

• Washington University-List of Phylogeny Software