TreeFam: a curated database of phylogenetic trees of animal gene families

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at and .

[1]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[2]  L. Robles,et al.  Boost of transmission at the pedicle of the incus in the chinchilla middle ear , 2007 .

[3]  A. Nuttall,et al.  Group delay of acoustic emissions in the ear. , 2006, Journal of neurophysiology.

[4]  Mario A Ruggero,et al.  Unexceptional sharpness of frequency tuning in the human cochlea. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  E. Koonin.  Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[6]  Alberto Recio-Spinoso,et al.  Delays of stimulus-frequency otoacoustic emissions and cochlear vibrations contradict the theory of coherent reflection filtering. , 2005, The Journal of the Acoustical Society of America.

[7]  Peer Bork,et al.  Consistency of genome‐based methods in measuring Metazoan evolution , 2005, FEBS letters.

[8]  Guy Perrière,et al.  Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases , 2005, Bioinform..

[9]  M. Ruggero,et al.  Wiener kernels of chinchilla auditory-nerve fibers: verification using responses to tones, clicks, and noise and comparison with basilar-membrane vibrations. , 2005, Journal of neurophysiology.

[10]  Paramvir S. Dehal,et al.  Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate , 2005, PLoS biology.

[11]  F. Delsuc,et al.  Phylogenomics and the reconstruction of the tree of life , 2005, Nature Reviews Genetics.

[12]  B. Haas,et al.  Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release , 2005, BMC Biology.

[13]  M. Göpfert,et al.  Tympanal travelling waves in migratory locusts , 2005, Journal of Experimental Biology.

[14]  Kimberly Van Auken,et al.  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics , 2004, Nucleic Acids Res..

[15]  Madeline A. Crosby,et al.  FlyBase: genes and gene models , 2004, Nucleic Acids Res..

[16]  Kara Dolinski,et al.  Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD) , 2004, Nucleic Acids Res..

[17]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[18]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[19]  Hiroaki Kitano,et al.  The PANTHER database of protein families, subfamilies, functions and pathways , 2004, Nucleic Acids Res..

[20]  Martin Vingron,et al.  The SYSTERS Protein Family Database in 2005 , 2004, Nucleic Acids Res..

[21]  Damian Smedley,et al.  Ensembl 2005 , 2004, Nucleic Acids Res..

[22]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[23]  Martijn A. Huynen,et al.  Evolutionary Diversity of Vertebrate Small Heat Shock Proteins , 2004, Journal of Molecular Evolution.

[24]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[25]  Mario A Ruggero,et al.  Comparison of group delays of 2f(1)-f(2) distortion product otoacoustic emissions and cochlear travel times. , 2004, Acoustics research letters online : ARLO.

[26]  Tianying Ren,et al.  Reverse propagation of sound in the gerbil cochlea , 2004, Nature Neuroscience.

[27]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[28]  Philip X Joris,et al.  Cochlear Phase and Amplitude Retrieved from the Auditory Nerve at Arbitrary Frequencies , 2003, The Journal of Neuroscience.

[29]  Christian E. V. Storm,et al.  Comprehensive analysis of orthologous protein domains using the HOPS database. , 2003, Genome research.

[30]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[31]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[32]  Bengt Sennblad,et al.  Bayesian gene/species tree reconciliation and orthology analysis using MCMC , 2003, ISMB.

[33]  Stefan Stenfelt,et al.  Basilar membrane and osseous spiral lamina motion in human cadavers with air and bone conduction stimuli , 2003, Hearing Research.

[34]  Jeffrey L Thorne,et al.  Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach , 2003, Genome Biology.

[35]  T. Ren.  Longitudinal pattern of basilar membrane vibration in the sensitive cochlea , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Edward H. Overstreet,et al.  Passive basilar membrane vibrations in gerbil neonates: mechanical bases of cochlear maturation , 2002, The Journal of physiology.

[37]  Sean R. Eddy,et al.  RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs , 2002, BMC Bioinformatics.

[38]  Christopher A Shera,et al.  Revised estimates of human cochlear tuning from otoacoustic and behavioral measurements , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Mario A Ruggero,et al.  Development of wide-band middle ear transmission in the Mongolian gerbil. , 2002, The Journal of the Acoustical Society of America.

[40]  F J Ayala,et al.  Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Sean R. Eddy,et al.  A simple algorithm to infer gene duplication and speciation events on a gene tree , 2001, Bioinform..

[42]  L. Robles,et al.  Mechanics of the mammalian cochlea. , 2001, Physiological reviews.

[43]  Sean R. Eddy,et al.  ATV: display and manipulation of annotated phylogenetic , 2001, Bioinform..

[44]  R. Schoonhoven,et al.  DPOAE group delays versus electrophysiological measures of cochlear delay in normal human ears. , 2001, The Journal of the Acoustical Society of America.

[45]  Feng-Chi Chen,et al.  Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. , 2001, American journal of human genetics.

[46]  Sunil Puria,et al.  Human middle-ear sound transfer function and cochlear input impedance , 2001, Hearing Research.

[47]  Alfred L Nuttall,et al.  Basilar membrane vibration in the basal turn of the sensitive gerbil cochlea , 2001, Hearing Research.

[48]  W. S. Rhode,et al.  Basilar membrane responses to broadband stimuli. , 2000, The Journal of the Acoustical Society of America.

[49]  M. Ruggero,et al.  Mechanical bases of frequency tuning and neural excitation at the base of the cochlea: comparison of basilar-membrane vibrations and auditory-nerve-fiber responses in chinchilla. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[50]  W. S. Rhode,et al.  Study of mechanical motions in the basal region of the chinchilla cochlea. , 2000, The Journal of the Acoustical Society of America.

[51]  J. Guinan,et al.  Auditory-nerve-fiber responses to high-level clicks: interference patterns indicate that excitation is due to the combination of multiple drives. , 2000, The Journal of the Acoustical Society of America.

[52]  Anthony W. Gummer,et al.  Evidence for active, nonlinear, negative feedback in the vibration response of the apical region of the in-vivo guinea-pig cochlea , 2000, Hearing Research.

[53]  G. Krohne,et al.  Subcellular distribution of the Xenopus p58/lamin B receptor in oocytes and eggs. , 1999, Journal of cell science.

[54]  H. Worman,et al.  The human lamin B receptor/sterol reductase multigene family. , 1998, Genomics.

[55]  E. Olson,et al.  Observing middle and inner ear mechanics with novel intracochlear pressure sensors. , 1998, The Journal of the Acoustical Society of America.

[56]  B. Kimberley,et al.  Age and the Human Cochlear Traveling Wave Delay , 1998, Ear and hearing.

[57]  J A Eisen,et al.  Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.

[58]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[59]  D. Irvine,et al.  First-spike timing of auditory-nerve fibers and comparison with auditory cortex. , 1997, Journal of neurophysiology.

[60]  L. Hood,et al.  Gene families: the taxonomy of protein paralogs and chimeras. , 1997, Science.

[61]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[62]  C. Köppl.  Phase Locking to High Frequencies in the Auditory Nerve and Cochlear Nucleus Magnocellularis of the Barn Owl, Tyto alba , 1997, The Journal of Neuroscience.

[63]  L. Robles,et al.  Basilar-membrane responses to tones at the base of the chinchilla cochlea. , 1997, The Journal of the Acoustical Society of America.

[64]  I. Russell,et al.  The location of the cochlear amplifier: spatial representation of a single tone on the guinea pig basilar membrane. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[65]  J. Eggermont,et al.  The effect of sound intensity on f1-sweep and f2-sweep distortion product otoacoustic emissions phase delay estimates in human adults. , 1997, The Journal of the Acoustical Society of America.

[66]  A. Nuttall,et al.  Steady-state sinusoidal velocity responses of the basilar membrane in guinea pig. , 1996, The Journal of the Acoustical Society of America.

[67]  M. Ruggero,et al.  Cochlear delays and traveling waves: comments on 'Experimental look at cochlear mechanics'. , 1994, Audiology : official organ of the International Society of Audiology.

[68]  J J Eggermont,et al.  Measuring human cochlear traveling wave delay using distortion product emission phase responses. , 1993, The Journal of the Acoustical Society of America.

[69]  F. Mammano,et al.  Biophysics of the cochlea: linear approximation. , 1993, The Journal of the Acoustical Society of America.

[70]  G. Donaldson,et al.  Derived band auditory brain-stem response estimates of traveling wave velocity in humans. I: Normal-hearing subjects. , 1993, The Journal of the Acoustical Society of America.

[71]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[72]  C W Ponton,et al.  Maturation of the traveling-wave delay in the human cochlea. , 1991, The Journal of the Acoustical Society of America.

[73]  P. D. Manley,et al.  Peripheral Hearing Mechanisms in Reptiles and Birds , 1990, Zoophysiology.

[74]  D. D. Greenwood.  A cochlear frequency-position function for several species--29 years later. , 1990, The Journal of the Acoustical Society of America.

[75]  G. Manley,et al.  Peripheral auditory processing in the bobtail lizard Tiliqua rugosa , 1990, Journal of Comparative Physiology A.

[76]  L. Carney,et al.  Temporal coding of resonances by low-frequency auditory nerve fibers: single-fiber responses and a population model. , 1988, Journal of neurophysiology.

[77]  M. Nei,et al.  Relationships between gene trees and species trees. , 1988, Molecular biology and evolution.

[78]  G. K. Yates,et al.  Auditory peripheral tuning: evidence for a simple resonance phenomenon in the lizard Tiliqua , 1988, Hearing Research.

[79]  W Jesteadt,et al.  Latency of auditory brain-stem responses and otoacoustic emissions using tone-burst stimuli. , 1988, The Journal of the Acoustical Society of America.

[80]  P. M. Narins,et al.  Frequency and time domain comparison of low-frequency auditory fiber responses in two anuran amphibians , 1987, Hearing Research.

[81]  M. Ruggero,et al.  Timing of spike initiation in cochlear afferents: dependence on site of innervation. , 1987, Journal of neurophysiology.

[82]  R. Klinke,et al.  Synchronized responses of primary auditory fibre-populations in Caiman crocodilus (L.) to single tones and clicks , 1986, Hearing Research.

[83]  A. Nuttall,et al.  High-synchrony cochlear compound action potentials evoked by rising frequency-swept tone bursts. , 1985, The Journal of the Acoustical Society of America.

[84]  P Dallos,et al.  Response characteristics of mammalian cochlear hair cells , 1985, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[85]  P. Narins,et al.  Neurophysiological evidence for a traveling wave in the amphibian inner ear. , 1984, Science.

[86]  E. D. Boer,et al.  Auditory physics. Physical principles in hearing theory. III , 1984 .

[87]  B. M. Johnstone,et al.  Measurement of basilar membrane motion in the guinea pig using the Mössbauer technique. , 1982, The Journal of the Acoustical Society of America.

[88]  L A Taber,et al.  Cochlear model including three-dimensional fluid and four modes of partition flexibility. , 1981, The Journal of the Acoustical Society of America.

[89]  James Lighthill,et al.  Energy flow in the cochlea , 1981, Journal of Fluid Mechanics.

[90]  J. Eggermont,et al.  Narrow-band analysis of compound action potentials for several stimulus conditions in the guinea pig , 1981, Hearing Research.

[91]  M Don,et al.  Analysis of the click-evoked brainstem potentials in humans using high-pass noise masking. II. Effect of click intensity. , 1980, The Journal of the Acoustical Society of America.

[92]  B. M. Johnstone,et al.  Single auditory neuron response during acute acoustic trauma , 1980, Hearing Research.

[93]  M. Ruggero.  Systematic errors in indirect estimates of basilar membrane travel times. , 1980, The Journal of the Acoustical Society of America.

[94]  J J Eggermont,et al.  Narrow-band AP latencies in normal and recruiting human ears. , 1979, The Journal of the Acoustical Society of America.

[95]  M. M. Gibson,et al.  Initial discharge latency and threshold considerations for some neurons in cochlear nuclear complex of the cat. , 1978, Journal of neurophysiology.

[96]  W. S. Rhode,et al.  Some observations on cochlear mechanics. , 1978, The Journal of the Acoustical Society of America.

[97]  J J Eggermont,et al.  Analysis of compound action potential responses to tone bursts in the human and guinea pig cochlea. , 1976, The Journal of the Acoustical Society of America.

[98]  C D Geisler,et al.  Transient response of the basilar membrane measured in squirrel monkeys using the Mössbauer effect. , 1976, The Journal of the Acoustical Society of America.

[99]  D. O. Kim,et al.  Cochlear nerve fiber responses: distribution along the cochlear partition. , 1975, The Journal of the Acoustical Society of America.

[100]  E D Young,et al.  Discharge patterns of single fibers in the pigeon auditory nerve. , 1974, Brain research.

[101]  E F Evans,et al.  The frequency response and other properties of single fibres in the guinea‐pig cochlear nerve , 1972, The Journal of physiology.

[102]  W. S. Rhode.  Observations of the vibration of the basilar membrane in squirrel monkeys using the Mössbauer technique. , 1971, The Journal of the Acoustical Society of America.

[103]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[104]  Russell R. Pfeiffer,et al.  Cochlear Nerve Fiber Discharge Patterns: Relationship to the Cochlear Microphonic , 1970, Science.

[105]  I. Whitfield.  Discharge Patterns of Single Fibers in the Cat's Auditory Nerve , 1966 .

[106]  D. C. Teas,et al.  Cochlear Responses to Acoustic Transients: An Interpretation of Whole-Nerve Action Potentials , 1962 .

[107]  M. Pryce,et al.  Wave Propagation and Group Velocity , 1961, Nature.

[108]  James L. Flanagan,et al.  Minimum Phase Responses for the Basilar Membrane , 1961 .

[109]  M Lawrence,et al.  A NOTE ON RECENT DEVELOPMENTS IN AUDITORY THEORY. , 1954, Proceedings of the National Academy of Sciences of the United States of America.

[110]  Georg v. Békésy,et al.  On the Resonance Curve and the Decay Period at Various Points on the Cochlear Partition , 1949 .

[111]  G. Békésy.  The Vibration of the Cochlear Partition in Anatomical Preparations and in Models of the Inner Ear , 1949 .

[112]  Georg v. Békésy,et al.  The Variation of Phase Along the Basilar Membrane with Sinusoidal Vibrations , 1947 .

[113]  H. Davis,et al.  Temporary deafness following exposure to loud tones and noise , 1946, Acta oto-laryngologica. Supplementum.

[114]  van Pim Dijk,et al.  Auditory Mechanisms: Processes and Models , 2006 .

[115]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[116]  P. Joris,et al.  The speed of auditory low-side suppression. , 2005, Journal of neurophysiology.

[117]  James A. Cuff,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[118]  Matthew Berriman,et al.  GeneDB: a resource for prokaryotic and eukaryotic organisms , 2004, Nucleic Acids Res..

[119]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database, 2004 updates , 2004, Nucleic Acids Res..

[120]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database , 2002, Nucleic Acids Res..

[121]  Masatoshi Nei,et al.  Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family. , 2002, Molecular biology and evolution.

[122]  Erik L. L. Sonnhammer,et al.  Automated ortholog inference from phylogenetic trees and calculation of orthology reliability , 2002, Bioinform..

[123]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[124]  Jozef J. Zwislocki,et al.  Auditory Sound Transmission: An Autobiographical Perspective , 2002 .

[125]  Nikos Kyrpides,et al.  Genomes OnLine Database (GOLD): a monitor of genome projects world-wide , 2001, Nucleic Acids Res..

[126]  S. Henikoff,et al.  Amino acid substitution matrices. , 2000, Advances in protein chemistry.

[127]  D. Parker,et al.  Measures of cochlear travelling wave delay in humans: I. Comparison of three techniques in subjects with normal hearing. , 1999, Acta oto-laryngologica.

[128]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[129]  M. Ruggero,et al.  Basilar-membrane responses to clicks at the base of the chinchilla cochlea. , 1998, The Journal of the Acoustical Society of America.

[130]  C. Köppl,et al.  Frequency tuning and spontaneous activity in the auditory nerve and cochlear nucleus magnocellularis of the barn owl Tyto alba. , 1997, Journal of neurophysiology.

[131]  M. Ruggero,et al.  The effect of intense acoustic stimulation on basilar-membrane vibrations , 1996 .

[132]  R. Fay.  Comparative Auditory Research , 1994 .

[133]  Richard R. Fay,et al.  Comparative Hearing: Mammals , 1994, Springer Handbook of Auditory Research.

[134]  Mario A. Ruggero,et al.  Basilar membrane responses to clicks , 1992 .

[135]  N. Saito.  The neighbor-joining method : A new method for reconstructing phylogenetic trees , 1987 .

[136]  E. Evans,et al.  Location-specific components of the gross cochlear action potential: an assessment of the validity of the high-pass masking technique by cochlear nerve fibre recording in the cat. , 1982, Audiology : official organ of the International Society of Audiology.

[137]  A. Krokstad,et al.  Noise-induced hearing losses. Can they be explained by basilar membrane movement? , 1979, Acta oto-laryngologica. Supplementum.

[138]  C. Fernández,et al.  Evoked electrical activity in the auditory nervous system , 1978 .

[139]  T. Gundersen,et al.  A study of the vibration of the basilar membrane in human temporal bone preparations by the use of the Mössbauer effect. , 1978, Acta oto-laryngologica.

[140]  C. Elberling,et al.  Action Potentirals Along the Cochlear Partition Recorded from the ear Canal in Man , 1974 .

[141]  J. E. Rose,et al.  Temporal position of discharges in single auditory nerve fibers within the cycle of a sine-wave stimulus: frequency and intensity effects. , 1971, The Journal of the Acoustical Society of America.

[142]  E. Bolinder.  The Fourier integral and its applications , 1963 .

[143]  B. P. Bogert,et al.  A Dynamical Theory of the Cochlea , 1950 .

[144]  Józef Zwislocki-Mościcki,et al.  Theorie der Schneckenmechanik: qualitative und quantitative Analyse , 1948 .