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PubMed2005

Adjusting EEG coherence for inter-electrode distance effects: an exploration in normal children.

Electroencephalographic (EEG) coherence between two points is strongly related to the distance between them, being inflated by volume conduction effects at short distances and reduced by signal phase differences at larger distances. This precludes simple comparison of coherence estimates involving different inter-electrode distances. We investigated adjusting coherence measures to remove such distance effects. After subtracting the estimated effects of random coherence due to volume conduction, exponential regression of the reduced coherence values against measured inter-electrode distance was used to estimate the remaining effects of inter-electrode distance. Residuals from this procedure were taken as coherences corrected for the systematic distance effects. These were adjusted to the mean reduced coherence level to avoid complexities in conceptualising negative residual coherences. It was found that systematic inter-electrode distance effects accounted for more than 50% of the variance remaining after removal of random coherence estimates. After these were also removed, substantial effects of EEG frequency band, different regions of the brain, and interhemispheric versus intrahemispheric values, as well as laterality effects within the latter, were obtained. Regional and frequency differences in adjusted coherence appear to reflect patterns expected from normal cortical development, but detailed understanding of more complex interactive effects is limited by the lack of relevant developmental data. Adjusting coherence values to remove systematic variability due to inter-electrode distances better represents cortico-cortical coupling and allows more efficient statistical analysis. This may contribute towards a better integration of coherence data in the EEG exploration of both normal and atypical brain functioning.

Brain↗
PubMed2005

Effects of different inter-implant distances on the stress distribution around endosseous implants in posterior mandible: a 3D finite element analysis.

PURPOSE: The aim of this study was to evaluate the effects of different inter-implant distances on stress distribution in the bone around the endosseous titanium implants under vertical, oblique and horizontal loads in the posterior mandibular edentulousim by finite element analysis (3D FEA). MATERIALS AND METHODS: 3D FEA models representing mandible and ITI implant (Straumann, Waldenburg, Switzerland) were simulated. The distances in-between the units were set at 0.5, 1.0 and 2.0 cm. Vertical (V) 70 degrees N, 60 degrees oblique (BL) 35 degrees N in buccolingual direction and horizontal (MD) 14 degrees N in mesiodistal direction loads were applied to each of these designs. The principal stresses (tensile and compressive stress) on each model were calculated using MSC MARC finite element analyze solver software. RESULTS: The tensile stress (P(max)) values have been evaluated that they rose at the cervical region of buccal side when the inter-implant distances increased under V and BL loads and they diminished while the inter-implant distances decreased. In short inter-implant distances the compressive stress (P(min)) has been presented with increased values and found at the lingual surface of the cervical region. DISCUSSION: The results of this study indicated that the magnitude of the stress was influenced by complex factors such as the direction of loads and the distance between adjacent fixtures. The stress occurring around fixtures differs significantly with various types of inter-implant distance. CONCLUSION: The evaluation of tensile and compressive stresses for cortical and cancellous bone under V, MD and BL loading conditions in aspect of inter-implant distance shows; the 1.0 cm of inter-implant distance is the optimum distance for two fixture implantation.

Computer Simulation↗
PubMed1985

A model of immunological distances in systematics.

While immunological distances among taxa have had wide use in systematics, there has been some doubt about their utility because of the observed non-metricity of such distance matrices. A model is presented here relating observed immunological distance to the actual number of antigenic site differences between taxa. This model accounts for the observed departures of these distances from the metric condition of reciprocity and triangle inequality. Based upon the model, two procedures are suggested for the transformation of immunological distances to metric distances appropriate for phylogenetic analysis. The model implies that the usual scaling adjustments applied to the immunological distance matrix are inappropriate; however, the same transformation applied instead to an initial similarity matrix will solve a scaling problem. Non-reciprocity of the distances is shown to remain a problem independent of this initial scaling problem. It is suggested that further transformation of these re-scaled distances may be obtained through an extension of the ADCLUS procedure developed in psychology. This approach suggests a general strategy for a transformation to metric distances, given a particular model of non-metricity for the data.

Epitopes↗
PubMed2004

Visual performance with multifocal intraocular lenses: mesopic contrast sensitivity under distance and near conditions.

OBJECTIVE: To evaluate distance and near visual performance under bright (photopic) and dim (mesopic) conditions in patients who had undergone uncomplicated cataract extraction with multifocal or monofocal intraocular lens (IOL) implantation. DESIGN: Prospective, nonrandomized, masked, comparative, observational case series. PARTICIPANTS: Thirty-two eyes of 32 patients after zonal-progressive multifocal IOL implantation (Allergan Medical Optics Array SA-40N) and 32 eyes of 32 age-matched patients after monofocal IOL implantation (Allergan Medical Optics SI-40NB). INTERVENTION: All eyes underwent phacoemulsification and IOL implantation. MAIN OUTCOME MEASURES: At 18 months after surgery, the monocular contrast sensitivity (CS) function was measured with sinusoidal grating charts at distance and near, at one photopic luminance level and 2 mesopic luminance levels (85, 5, and 2.5 candelas per square meter). RESULTS: Under bright conditions, CS at distance in the multifocal group was not statistically different (P>0.01) from that in the monofocal group at any tested grating spatial frequency (1.5, 3, 6, 12, and 18 cycles per degree [cpd]). At low luminances, distance CS for the multifocal group was worse than that for the monofocal group at the highest test spatial frequencies (12 and 18 cpd; P<0.01). At near, photopic CS in the multifocal group was lower than at distance; patients with only a monofocal distance correction, however, could not detect the test gratings, even at the highest available contrast. With optimal near spectacle additions (i.e., using the distance correction of the multifocal IOL), there were no significant differences between the photopic near CS values for the multifocal and monofocal groups. When the luminance was decreased, near CS at all spatial frequencies was reduced in both groups. Contrast sensitivity in the near-corrected, multifocal group was significantly worse than in the near-corrected, monofocal group at high spatial frequencies (12 and 18 cpd). CONCLUSIONS: This work supports the findings of earlier authors that the Array multifocal IOL, with its center-distance design, is distance biased. Distance CS is within normal limits under bright photopic conditions but shows deficits at higher spatial frequencies (more than approximately 12 cpd) under dim mesopic conditions. Near CS obtained with the multifocal IOL is below that which can be achieved by an appropriate monofocal near correction, for all spatial frequencies and illumination conditions.

Aged↗
PubMed1988

Distance distributions in proteins recovered by using frequency-domain fluorometry. Applications to troponin I and its complex with troponin C.

We used resonance energy transfer to examine the distribution of distances between two sites on troponin I (TnI). The donor (D) was the single tryptophan residue at site 158 (Trp 158), and the acceptor (A) was cysteine 133 (Cys 133) which was labeled with N-(iodoacetyl)-N'-(1-sulfo-5-naphthyl)ethylenediamine (IE). A distribution of D-A distances results in a distribution of donor decay times, which were resolved by using frequency-domain fluorometry. In the native state we recovered a relatively narrow distribution of D-A distances. The widths of the distance distributions were found to increase progressively and dramatically with increasing concentrations of guanidine hydrochloride. Binding of calcium-free troponin C (TnC) to troponin I did not alter the distance distribution. Addition of Ca2+ to the TnI.TnC complex resulted in a sharper distance distribution and protected against the guanidine hydrochloride induced increase in the width of the distance distribution. Additionally, the same distance distributions were recovered for native and denatured TnI when the Forster distance for energy transfer was decreased by acrylamide quenching. These results demonstrate that distance distributions can be recovered with good accuracy, to the extent of revealing modest changes due to binding of other components. This technique should have widespread applications in studies of protein folding.

Fluorometry↗
PubMed2001

Functional projection distances of spinal interneurons mediating reciprocal inhibition during swimming in Xenopus tadpoles.

The basis for longitudinal coordination among spinal neurons during locomotion is still poorly understood. We have now examined the functional projection distances for the longitudinal axons of reciprocal inhibitory 'commissural interneurons' in the spinal cord of young Xenopus tadpoles. In quiescent animals, glycinergic inhibitory postsynaptic potentials (IPSPs) were evoked in ventral spinal neurons by stimulating small rostral and caudal groups of commissural interneuron somata at different distances on the opposite side of the hindbrain and spinal cord. Unitary IPSPs, produced by single synaptic contacts, could be distinguished from background noise. Local cord stimulation at different distances revealed maximum functional projection distances up to approximately 0.5 mm for both descending and ascending axons, but with the probability of recording connections falling steeply over this distance. These maximum longitudinal projection distances are smaller than predicted by axonal anatomy (approximately 1.2 mm). We then measured functional projection distances during swimming by examining the synaptic output of a surgically isolated group of rostral commissural interneurons, mapping the occurrence of the mid-cycle, reciprocal IPSPs they produced in more caudal neurons. IPSPs occurred with high probability up to 0.9 mm away, nearly twice the projection distance found in quiescent tadpoles. These results show that synaptic contacts from commissural interneurons could influence longitudinal coupling during swimming at distances of up to 0.9 mm (approximately 4-5 myotome segments or approximately 25% of the spinal cord). They provide direct evidence for functional projection distances of a characterized class of interneurons belonging to a spinal locomotor pattern generator.

Animals↗
PubMed1989

Effects of room reflectance and background noise on perceived auditory distance.

Perceptions of egocentric auditory distance were investigated within an environment for which the reverberation time could be systematically varied without changes in the size or shape of the room. Two levels of wide-band background noise, differing by 20 dB, were used as a masking stimulus. Target sounds were presented from distances between 0.75 and 6.0 m and verbal reports of distance were collected from 288 listeners in two separate experiments. Changes in physical distance produced variation in reported distance in each configuration. Reported distance was generally proportional to real distance, but considerably underestimated when room reflectance was low. When room reflectance was high (T60 approximately 1.7 s for the range of frequencies used), initial reports of distance were often overestimates; upon repeated presentation, judgments in the high reflectance room became more nearly veridical. The effect of increasing the background noise level was to decrease the perceived distance. These findings are in accord with expectations based upon the importance of reverberation cue(s) to distance and upon previous analyses from this laboratory.

Acoustics↗
PubMed1991

Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures.

Solution structures for many proteins have been determined to date utilizing interproton distance constraints estimated from two-dimensional nuclear Overhauser effect (2D NOE) spectra. Although the simple isolated spin pair approximation (ISPA) generally used can result in systematic errors in distances, the large number of constraints enables protein structure to be defined with reasonably high resolution. Effects of these systematic errors on the resulting protein structure are examined. Iterative relaxation matrix calculations, which account for dipolar interactions between all protons in a molecule, can accurately determine internuclear distances with little or no a priori knowledge of the molecular structure. The value of this additional complexity is also addressed. To assess these distance determination methods, hypothetical "experimental" data, including random noise and peak overlap, are calculated for an arbitrary "true" protein structure. Three methods of obtaining distance constraints from 2D NOE peak intensities are examined: one entails a conservative use of ISPA, one assumes the ISPA to be fairly accurate, and one utilizes an iterative relaxation matrix method called MARDIGRAS (matrix analysis of relaxation for discerning the geometry of an aqueous structure), developed in this laboratory. A distance geometry algorithm was used to generate a family of structures for each distance set. The quality of the average structure from each family was good. The root-mean-square deviation of that average structure from the true structure was improved about 2-5% using the more restrictive rather than the more conservative ISPA approach. Use of MARDIGRAS in a conservative fashion--i.e., with a poor initial model--resulted in improvement in the root-mean-square deviation by 8-15%. With a better initial model, MARDIGRAS obtained even more accurate distances. MARDIGRAS also permits analysis of 2D NOE data at longer mixing times, yielding additional distances. Use of more restrictive ISPA distances did, however, result in a few systematically incorrect structural features in local regions of the protein, producing distortions of 2-3 A. Comparison between experimental data and spectra calculated for the structures correlates with root-mean-square deviation, offering a method of structure evaluation. An R factor for evaluating fit between experimental and calculated 2D NOE intensities is proposed.

Magnetic Resonance Spectroscopy↗
PubMed1998

Genetic distances and ordination: the land snail Helix aspersa in north Africa as a test case.

We examined the efficiencies of ordination methods in the treatment of gene frequency data at intraspecific level, using metric and nonmetric distance measures (Nei's and Rogers' genetic distances, chi 2 distance). We assessed initial processes responsible for the geographical distribution of the Mediterranean land snail Helix aspersa. Seventeen enzyme loci from 30 North African snail populations were considered in the present analysis. Five combinations of distance/multivariate analysis were compared: correspondence analysis (CA), nonmetric multidimensional scaling (NMDS) on Nei's, Rogers', and chi 2 distances, and principal coordinates analysis on Rogers' distances. Configuration of the objects resulting from ordination was projected onto three-dimensional graphics with the minimum spanning tree or the relative neighborhood graph superimposed. Pre- and postordination or clustering distance matrices were compared by means of correlation methods. As expected, all combinations led to a clear west versus east pattern of variation. However, the intraregional relationships and degree of connectivity between pairs of operational taxonomic units were not necessarily constant from one method to another. Ordination methods when applied with Nei's and Rogers' distances provided the best fit, with original distances (r = 0.98) compared with UPGMA clustering (r approximately 0.75). The Nei/NMDS combination seems to be a good compromise (distortion index dt = 10%) between Rogers/NMDS, which produces a more confusing pattern of differentiation (dt = 24%), and chi 2/CA, which tends to distort large distances (dt = 31%). NMDS obviously provides a powerful method to summarize relationships between populations, when neither hierarchical structure nor phylogenetic inference are required. These findings led the discussion on the good performance of NMDS, the appropriate distances to be used, and the potential application of this method to other types of allelic data (such as microsatellite loci) or data on nucleotide sequences of genes.

Africa, Northern↗
PubMed2005

The choice of optimal distance measure in genome-wide datasets.

MOTIVATION: Many types of genomic data are naturally represented as binary vectors. Numerous tasks in computational biology can be cast as analysis of relationships between these vectors, and the first step is, frequently, to compute their pairwise distance matrix. Many distance measures have been proposed in the literature, but there is no theory justifying the choice of distance measure. RESULTS: We examine the approaches to measuring distances between binary vectors and study the characteristic properties of various distance measures and their performance in several tasks of genome analysis. Most distance measures between binary vectors turn out to belong to a single parametric family, namely generalized average-based distance with different exponents. We show that descriptive statistics of distance distribution, such as skewness and kurtosis, can guide the appropriate choice of the exponent. On the contrary, the more familiar distance properties, such as metric and additivity, appear to have much less effect on the performance of distances. AVAILABILITY: R code GADIST and Supplementary material are available at http://research.stowers-institute.org/bioinfo/

Algorithms↗
PubMed2003

Factors affecting the errors in the estimation of evolutionary distances between sequences.

Phylogenetic methods that use matrices of pairwise distances between sequences (e.g., neighbor joining) will only give accurate results when the initial estimates of the pairwise distances are accurate. For many different models of sequence evolution, analytical formulae are known that give estimates of the distance between two sequences as a function of the observed numbers of substitutions of various classes. These are often of a form that we call "log transform formulae". Errors in these distance estimates become larger as the time t since divergence of the two sequences increases. For long times, the log transform formulae can sometimes give divergent distance estimates when applied to finite sequences. We show that these errors become significant when t approximately 1/2 |lambda(max)|(-1) logN, where lambda(max) is the eigenvalue of the substitution rate matrix with the largest absolute value and N is the sequence length. Various likelihood-based methods have been proposed to estimate the values of parameters in rate matrices. If rate matrix parameters are known with reasonable accuracy, it is possible to use the maximum likelihood method to estimate evolutionary distances while keeping the rate parameters fixed. We show that errors in distances estimated in this way only become significant when t approximately 1/2 |lambda(1)|(-1) logN, where lambda(1) is the eigenvalue of the substitution rate matrix with the smallest nonzero absolute value. The accuracy of likelihood-based distance estimates is therefore much higher than those based on log transform formulae, particularly in cases where there is a large range of timescales involved in the rate matrix (e.g., when the ratio of transition to transversion rates is large). We discuss several practical ways of estimating the rate matrix parameters before distance calculation and hence of increasing the accuracy of distance estimates.

Evolution, Molecular↗
PubMed2000

How much guidewire is too much? Direct measurement of the distance from subclavian and internal jugular vein access sites to the superior vena cava-atrial junction during central venous catheter placement.

OBJECTIVE: The introduction of excessive lengths of guidewire during placement of central venous catheters from the internal jugular vein (IJV) or the subclavian vein (SCV) can result in rare but significant complications. To identify a "safe" guidewire insertion length, the authors performed direct intravascular measurement of the distance from these venous access sites to the superior vena cava-atrial junction (CAJ), and evaluated these distances relative to the patients' height, weight, sex, and chest radiographs. DESIGN: Prospective, nonrandomized observation. SETTING: The Interventional Radiology Department of a tertiary care referral hospital. PATIENTS: 100 adults (45 women, 55 men) evaluated during fluoroscopically directed central venous catheter placement. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The distance from the IJV or SCV access site was directly measured using fluoroscopy and an intravascular guidewire. 40 right IJVs, 31 right SCVs, 16 left SCVs, and 13 left IJVs were studied. Comparative measurements from the postprocedure radiograph were made in 20 of these cases. All measurements were correlated with patient sex, height, and weight. The mean distance from all access sites to the superior vena cava-atrial junction was 18.0 cm. The right IJV distance was the shortest, averaging 16 cm. The left SCV distance was the longest, averaging 21.2 cm. Right SCV and left IJV distances were 18.4 and 19.1 cm, respectively, but this difference was not statistically significant. Weight and radiographic measurements did not correlate with the measured vascular distance, although there was a trend toward longer distances in taller patients and males. CONCLUSIONS: Patient height, weight, and measurements from previous chest radiographs are less reliable in predicting a safe wire length than is the access site selected. In most cases, 18 cm should be considered the upper limit of guidewire introduced during central catheter placement in adults. The guidewires supplied in catheter kits should have lengths correlated to those of the catheters, and should have distance markings printed upon them.

Catheterization, Central Venous↗
PubMed2005

Social and geographic distance in HIV risk.

OBJECTIVE: The objective of this study was to examine the relationship between social distance (measured as the geodesic, or shortest distance, between 2 people in a connected network) and geographic distance (measured as the actual distance between them in kilometers [km]). STUDY: We used data from a study of 595 persons at risk for HIV and their sexual and drug-using partners (total N = 8920 unique individuals) conducted in Colorado Springs, Colorado, from 1988 to 1992--a longitudinal cohort study that ascertained sociodemographic, clinical, behavioral, and network information about participants. We used place of residence as the geographic marker and calculated distance between people grouped by various characteristics of interest. RESULTS: Fifty-two percent of all dyads were separated by a distance of 4 km or less. The closest pairs were persons who both shared needles and had sexual contact (mean = 3.2 km), and HIV-positive persons and their contacts (mean = 2.9). The most distant pairs were prostitutes and their paying partners (mean = 6.1 km). In a connected subset of 348 respondents, almost half the persons were between 3 and 6 steps from each other in the social network and were separated by a distance of 2 to 8 km. Using block group centroids, the mean distance between all persons in Colorado Springs was 12.4 km compared with a mean distance of 5.4 km between all dyads in this study (P <0.0001). The subgroup of HIV-positive people and their contacts was drawn in real space on a map of Colorado Springs and revealed tight clustering of this group in the downtown area. CONCLUSION: The association of social and geographic distance in an urban group of people at risk for HIV provides demonstration of the importance of geographic clustering in the potential transmission of HIV. The proximity of persons connected within a network, but not necessarily known to each other, suggests that a high probability of partner selection from within the group may be an important factor in maintenance of HIV endemicity.

Cluster Analysis↗
PubMed2004

Markov edit distance.

Edit distance was originally developed by Levenstein several decades ago to measure the distance between two strings. It was found that this distance can be computed by an elegant dynamic programming procedure. The edit distance has played important roles in a wide array of applications due to its representational efficacy and computational efficiency. To effect a more reasonable distance measure, the normalized edit distance was proposed. Many algorithms and studies have been dedicated along this line with impressive performances in recent years. There is, however, a fundamental problem with the original definition of edit distance that has remained elusive: its context-free nature. In determining the possible actions, i.e., insertion, deletion, and substitution, no systematic consideration was given to the local behaviors of the string/pattern in question that indeed encompass great amount of useful information regarding its content. In this paper, inspired by the success of the Markov Random Field theory, a new edit distance called Markov edit distance (MED) within the dynamic programming framework is proposed to take full advantage of the local statistical dependencies in the pattern in order to arrive at enhanced matching performance. Within this framework, two specialized distance measures are developed: The reshuffling MED to handle cases where a subpattern in the target pattern is the reshuffles of that in the source pattern, and the coherence MED which is able to incur local content based substitution, insertion, and deletion. The applications based on these two MEDs in string matching are then explored, whereof encouraging empirical results have been observed.

Algorithms↗
PubMed1994

Muscle activation patterns for reaching: the representation of distance and time.

1. The timing and intensity of phasic muscle activation were related to the distance of reaching movements of the human arm. We dissociated phasic components of muscle activation from complete muscle activation waveforms by subtracting waveforms obtained during very slow movements. 2. We recorded electromyographic (EMG) activity from elbow and/or shoulder muscles as standing subjects reached forward and upward to targets at four distances. Accuracy was deemphasized and no terminal corrections were allowed. In the first part of the experiment subjects were asked to move at their preferred speed. In the second part of the experiment they were asked to move using a range of speeds. 3. In the first part of the experiment subjects moved faster to more distant targets but they also increased movement time as a nearly linear function of target distance. The slope of this function was very similar across subjects. The phasic EMG waveforms for different distances appeared to be similar in shape but of variable duration. EMG time base was quantified using a correlation technique that identified the time base scale factor that best superimposed a given trace with a template. This technique revealed that the slope of the relation between EMG time base and target distance was not the same for all muscles. 4. In the second part of the experiment, where subjects moved to each target at a range of specified speeds, time base scaling was again significantly different for different muscles. The scaling differed most dramatically between anterior deltoid and medial head of triceps. 5. EMG intensity was more strongly related to movement time than to distance. We quantified the correspondence of distance and movement time to phasic EMG intensity using a multiple regression analysis of all distances and speeds, assuming a power relation. Distance exponents were positive and movement time exponents were larger and negative. This implies that movement time is more important than distance in its relation to EMG intensity.

Adult↗
PubMedDate not supplied

Bilateral medial rectus recession in convergence excess esotropia, with and without distance orthophoria.

PURPOSE: To evaluate the effectivity and safety of bilateral medial rectus recession for the correction of acquired convergence excess esotropia, with and without distance orthophoria. METHODS: Thirty-five pediatric patients with acquired convergence excess esotropia were operated with bilateral medial rectus recessions based on the near angle measured through the distance correction. Preoperatively, in 26 patients, full hypermetropic correction did not fully correct the distance angle; these patients were operated for the residual angle for distance and near. In nine patients full hypermetropic correction produced distance orthophoria and these cases also had near orthophoria through a near add; these patients could have used bifocals, but surgery was chosen instead. RESULTS: Postoperatively, 19 of the 26 patients with distance esotropia (73%) and 6 of the 9 with distance orthophoria (66.6%) were successfully aligned. Consecutive exotropia developed in two patients (7.6%) in the distance esotropia group and one (11.1%) in the distance orthophoria group. CONCLUSIONS: These results suggest that bilateral recession of the medial recti based on the near deviation is effective in eliminating the near angle in convergence excess esotropia. In patients with distance orthophoria this operation can be used as an initial treatment instead of bifocals. Although the risk of consecutive exotropia was low in this series, a larger number of patients would determine its actual rate more accurately.

Child↗
PubMed2005

Scoredist: a simple and robust protein sequence distance estimator.

BACKGROUND: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used. RESULTS: We propose a correction-based protein sequence estimator called Scoredist. It uses a logarithmic correction of observed divergence based on the alignment score according to the BLOSUM62 score matrix. We evaluated Scoredist and a number of optimal matrix methods using three evolutionary models for both training and testing Dayhoff, Jones-Taylor-Thornton, and Muller-Vingron, as well as Whelan and Goldman solely for testing. Test alignments with known distances between 0.01 and 2 substitutions per position (1-200 PAM) were simulated using ROSE. Scoredist proved as accurate as the optimal matrix methods, yet substantially more robust. When trained on one model but tested on another one, Scoredist was nearly always more accurate. The Jukes-Cantor and Kimura correction methods were also tested, but were substantially less accurate. CONCLUSION: The Scoredist distance estimator is fast to implement and run, and combines robustness with accuracy. Scoredist has been incorporated into the Belvu alignment viewer, which is available at ftp://ftp.cgb.ki.se/pub/prog/belvu/.

Algorithms↗
PubMed2006

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called delta value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. delta values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their delta values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. delta values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference.

Algorithms↗