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](www.dnathink.org)huangzhiman 2003.3.15  \nDATA ANALYSIS IN MOLECULAR BIOLOGY AND EVOLUTION  \nby  \nXuhua Xia  \nUniversity of Hong Kong  \nKLUWER ACADEMIC PUBLISHERS  \nNEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW  \neBook ISBN: 0-306-46893-X  \nPrint ISBN: 0-792-37500-9  \n©2002 Kluwer Academic Publishers  \nNew York, Boston, Dordrecht, London, Moscow  \nPrint ©2000 Kluwer Academic / Plenum Publishers New York  \nAll rights reserved  \nNo part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher  \nCreated in the United States of America  \nVisit Kluwer Online at: [http://kluweronline.com](http://kluweronline.com)  \nand Kluwer's eBookstore at: [http://ebooks.kluweronline.com](http://ebooks.kluweronline.com)  \nContents  \nACKNOWLEDGEMENTS ................................................................................ XI  \nPREFACE ........................................................................................................... XIII  \n1. INSTALLATION OF DAMBE AN D A QUICK START...........................1  \n1. INSTALLATION............................................................................................. 1  \n2. A JUMP START ............................................................................................ 2  \n2. FILE CONVERSION....................................................................................7  \n1. A PLETHORA OF COMPUTER PROGRAMS ............................................. 8  \n2. A PLETHORA OF SEQUENCE FORMATS ....................................................... 8  \n3. READSEQ.................................................................................................... 9  \n4. FILE CONVERSION USING DAMBE............................................................ 10  \n4.1 Convert all sequencesfrom oneformat to another.............................. 11  \n4.2 Converting a subset of sequences....................................................... 12  \n4.3 Output PHYLTEST files....................................................................... 13  \n3. PROCESSING GENBANK FILES............................................................ 17  \n1. GENBANK FILE FORMAT ............................................................................18  \n2. REANDING GENBANK FILES WITH DAMBE..................................................20  \n4. ACCESSING GENBANK OR NETWORKED COMPUTERS ..............25  \n1. INTRODUCTION..........................................................................................25  \n2. READING MOLECULAR SEQUENCES DIRECTLY FROM GENBANK...............25  \n3. READING FROM AND WRITING TO ANOTHER NETWORKED COMPUTER .......30  \nvi Contents  \n4. EXERCISE ..................................................................................................32  \n5. PAIR-WISE AND MULTIPLE SEQUENCE ALIGNMENT..................33  \n1. INTRODUCTION..........................................................................................33  \n1.1 The dot-matrix approach.......................................................................33  \n1.2 Similarity or distance method...............................................................36  \n2. SEQUENCE ALIGNMENT USING DAMBE....................................................37  \n2.1 Align nucleotide or ammo acid sequences ..........................................37  \n2.2 Align nucleotide sequences against amino acid sequences.................38  \n6. FACTORS AFFECTING NUCLEOTIDE FREQUENCIES...................41  \n1. INTRODUCTION..........................................................................................41  \n1.1 The frequency parameters....................................................................41  \n1.2 Factors that might change the frequency parameters..........................42  \n1.3 Frequency parameters and ph","cbCaipWH8D7np00r","https://ap.wps.com/l/cbCaipWH8D7np00r","pdf",7877667,284,"English","# Contents\n## Acknowledgements and Preface\n## Installation of DAMBE and a Quick Start\n### Installation\n### A Jump Start\n### File Conversion\n## Processing GenBank Files\n## Accessing GenBank or Networked Computers\n## Pair-wise and Multiple Sequence Alignment\n## Sequence Alignment Using DAMBE\n## Factors Affecting Nucleotide Frequencies\n## Counting Nucleotide and Dinucleotide Frequencies\n## Case Study 1: Arthropod Phylogeny\n## Factors Affecting Codon Frequencies\n## Case Study 2: Transcription and Codon Usage Bias\n## Case Study 3: Translation and Codon Usage Bias","[{\"question\":\"What topics are covered about DAMBE in the early chapters?\",\"answer\":\"The contents include installing DAMBE, starting with basic use, and performing file conversion workflows using DAMBE.\"},{\"question\":\"How does the book handle GenBank sequence data?\",\"answer\":\"It outlines the GenBank file format and how to read GenBank files with DAMBE, including accessing sequences from networked computers.\"},{\"question\":\"Which analytical methods and case studies are included?\",\"answer\":\"It covers pair-wise and multiple sequence alignment, nucleotide and codon frequency analysis, and case studies such as arthropod phylogeny and transcription/translation codon-usage bias.\"}]","DATA ANALYSIS IN MOLECULAR BIOLOGY AND EVOLUTION - Contents - Introduction to DAMBE and sequence data workflows | PDF",1789975413,716]