Class information for:
Level 1: CODON MODELS//POSITIVE SELECTION//MOLECULAR BIOLOGY AND EVOLUTION

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
10256 1078 47.1 84%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
90 3       MATHEMATICAL & COMPUTATIONAL BIOLOGY//BIOINFORMATICS//BMC BIOINFORMATICS 77178
126 2             MOLECULAR BIOLOGY AND EVOLUTION//BIOINFORMATICS//MATHEMATICAL & COMPUTATIONAL BIOLOGY 23963
10256 1                   CODON MODELS//POSITIVE SELECTION//MOLECULAR BIOLOGY AND EVOLUTION 1078

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 CODON MODELS authKW 768093 4% 68% 40
2 POSITIVE SELECTION authKW 482331 14% 11% 152
3 MOLECULAR BIOLOGY AND EVOLUTION journal 276368 22% 4% 233
4 CODON SUBSTITUTION MODEL authKW 241362 1% 61% 14
5 DN DS authKW 207683 2% 33% 22
6 BRANCH SITE MODEL authKW 181273 1% 80% 8
7 PROTEIN EVOLUTION authKW 166836 6% 9% 66
8 SYNONYMOUS SUBSTITUTION authKW 139021 2% 27% 18
9 BRANCH SITE TEST authKW 113297 0% 100% 4
10 CLADE MODEL authKW 113297 0% 100% 4

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 Evolutionary Biology 61953 50% 0% 538
2 Genetics & Heredity 26763 65% 0% 697
3 Biochemistry & Molecular Biology 4351 53% 0% 568
4 Mathematical & Computational Biology 3944 11% 0% 122
5 Biochemical Research Methods 758 10% 0% 104
6 Biotechnology & Applied Microbiology 691 12% 0% 129
7 Biology 312 5% 0% 59
8 Statistics & Probability 45 2% 0% 23
9 Ecology 23 3% 0% 30
10 Biophysics 10 2% 0% 25

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 URM 5506 84973 0% 100% 3
2 BIOINFORMAT MOL EVOLUT GRP 42478 1% 25% 6
3 EA 3781 EVOLUT BIOL 37764 0% 67% 2
4 EHLTH INNOVAT PLATFORM 37764 0% 67% 2
5 ADV COMPUTAT SCI SYNTHET BIOL TEAM 28324 0% 100% 1
6 ATERLIER BIOINFORMAT 28324 0% 100% 1
7 BASIC SCI BASIC SCI 28324 0% 100% 1
8 BIO ERS EVOLUCAO MOL 28324 0% 100% 1
9 BIOINFORMAT PHARMACOGENET 28324 0% 100% 1
10 BIOINFORMAT PHARMACOGENOMICS 28324 0% 100% 1

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 MOLECULAR BIOLOGY AND EVOLUTION 276368 22% 4% 233
2 JOURNAL OF MOLECULAR EVOLUTION 51187 8% 2% 83
3 BMC EVOLUTIONARY BIOLOGY 22939 5% 2% 52
4 GENOME BIOLOGY AND EVOLUTION 17615 3% 2% 29
5 EVOLUTIONARY BIOINFORMATICS 12925 1% 4% 12
6 BIOLOGY DIRECT 8615 1% 2% 13
7 SYSTEMATIC BIOLOGY 5400 1% 1% 16
8 BMC BIOINFORMATICS 3350 3% 0% 30
9 GENETICS 2985 3% 0% 37
10 PLOS COMPUTATIONAL BIOLOGY 2667 2% 0% 21

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 CODON MODELS 768093 4% 68% 40 Search CODON+MODELS Search CODON+MODELS
2 POSITIVE SELECTION 482331 14% 11% 152 Search POSITIVE+SELECTION Search POSITIVE+SELECTION
3 CODON SUBSTITUTION MODEL 241362 1% 61% 14 Search CODON+SUBSTITUTION+MODEL Search CODON+SUBSTITUTION+MODEL
4 DN DS 207683 2% 33% 22 Search DN+DS Search DN+DS
5 BRANCH SITE MODEL 181273 1% 80% 8 Search BRANCH+SITE+MODEL Search BRANCH+SITE+MODEL
6 PROTEIN EVOLUTION 166836 6% 9% 66 Search PROTEIN+EVOLUTION Search PROTEIN+EVOLUTION
7 SYNONYMOUS SUBSTITUTION 139021 2% 27% 18 Search SYNONYMOUS+SUBSTITUTION Search SYNONYMOUS+SUBSTITUTION
8 BRANCH SITE TEST 113297 0% 100% 4 Search BRANCH+SITE+TEST Search BRANCH+SITE+TEST
9 CLADE MODEL 113297 0% 100% 4 Search CLADE+MODEL Search CLADE+MODEL
10 GENE COMPACTNESS 113297 0% 100% 4 Search GENE+COMPACTNESS Search GENE+COMPACTNESS

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref.
in cl.		 Shr. of ref. in
cl.		 Citations
1 ANISIMOVA, M , KOSIOL, C , (2009) INVESTIGATING PROTEIN-CODING SEQUENCE EVOLUTION WITH PROBABILISTIC CODON SUBSTITUTION MODELS.MOLECULAR BIOLOGY AND EVOLUTION. VOL. 26. ISSUE 2. P. 255 -271 89 59% 72
2 YANG, ZH , (2007) PAML 4: PHYLOGENETIC ANALYSIS BY MAXIMUM LIKELIHOOD.MOLECULAR BIOLOGY AND EVOLUTION. VOL. 24. ISSUE 8. P. 1586 -1591 27 48% 3661
3 ECHAVE, J , SPIELMAN, SJ , WILKE, CO , (2016) CAUSES OF EVOLUTIONARY RATE VARIATION AMONG PROTEIN SITES.NATURE REVIEWS GENETICS. VOL. 17. ISSUE 2. P. 109 -121 58 44% 11
4 DELPORT, W , SCHEFFLER, K , SEOIGHE, C , (2009) MODELS OF CODING SEQUENCE EVOLUTION.BRIEFINGS IN BIOINFORMATICS. VOL. 10. ISSUE 1. P. 97 -109 62 68% 24
5 MURRELL, B , WEAVER, S , SMITH, MD , WERTHEIM, JO , MURRELL, S , AYLWARD, A , EREN, K , POLLNER, T , MARTIN, DP , SMITH, DM , ET AL (2015) GENE-WIDE IDENTIFICATION OF EPISODIC SELECTION.MOLECULAR BIOLOGY AND EVOLUTION. VOL. 32. ISSUE 5. P. 1365 -1371 25 96% 18
6 POND, SLK , MURRELL, B , FOURMENT, M , FROST, SDW , DELPORT, W , SCHEFFLER, K , (2011) A RANDOM EFFECTS BRANCH-SITE MODEL FOR DETECTING EPISODIC DIVERSIFYING SELECTION.MOLECULAR BIOLOGY AND EVOLUTION. VOL. 28. ISSUE 11. P. 3033 -3043 28 82% 107
7 SPIELMAN, SJ , WAN, SY , WILKE, CO , (2016) A COMPARISON OF ONE-RATE AND TWO-RATE INFERENCE FRAMEWORKS FOR SITE-SPECIFIC DN/DS ESTIMATION.GENETICS. VOL. 204. ISSUE 2. P. 499 -+ 30 79% 2
8 ANISIMOVA, M , LIBERLES, DA , (2007) THE QUEST FOR NATURAL SELECTION IN THE AGE OF COMPARATIVE GENOMICS.HEREDITY. VOL. 99. ISSUE 6. P. 567 -579 68 45% 46
9 BLOOM, JD , (2017) IDENTIFICATION OF POSITIVE SELECTION IN GENES IS GREATLY IMPROVED BY USING EXPERIMENTALLY INFORMED SITE-SPECIFIC MODELS.BIOLOGY DIRECT. VOL. 12. ISSUE . P. - 48 55% 0
10 ALVAREZ-PONCE, D , SABATER-MUNOZ, B , TOFT, C , RUIZ-GONZALEZ, MX , FARES, MA , (2016) ESSENTIALITY IS A STRONG DETERMINANT OF PROTEIN RATES OF EVOLUTION DURING MUTATION ACCUMULATION EXPERIMENTS IN ESCHERICHIA COLI.GENOME BIOLOGY AND EVOLUTION. VOL. 8. ISSUE 9. P. 2914 -2927 50 52% 0

Classes with closest relation at Level 1


Rank Class id link
1 13045 ISOCHORES//EVOLUZ MOL//MALE MUTATION BIAS
2 8300 WHOLE GENOME DUPLICATION//GENOME DUPLICATION//GENE DUPLICATION
3 922 SYSTEMATIC BIOLOGY//PHYLOGENETIC NETWORK//PHYLOGENETIC TREE
4 2640 SELECTIVE SWEEP//MCDONALD KREITMAN TEST//GENETICS
5 19783 EXPRESSION EVOLUTION//TRANS REGULATION//CIS REGULATORY DIVERGENCE
6 20039 ORTHOLOGY//BIDIRECTIONAL BEST HIT//GENOME FUNCTIONAL PREDICTION
7 16263 INTRALOCUS SEXUAL CONFLICT//SEX BIASED GENE EXPRESSION//SEXUAL ANTAGONISM
8 2829 CODON USAGE//CODON USAGE BIAS//SYNONYMOUS CODON USAGE
9 5407 EXPERIMENTAL EVOLUTION//BENEFICIAL MUTATIONS//CLONAL INTERFERENCE
10 17055 CORRELATED MUTATIONS//DIRECT COUPLING ANALYSIS//INVERSE ISING PROBLEM

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