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PubMed2006

The national continuous quality improvement tool for mental health education: results of targeted and supported implementation in England.

The national continuous quality assurance tool for mental health education and training has recently been developed. This paper describes the planned implementation of the tool across NHS Workforce Development Confederations (WDCs) in England. Large stakeholder groups in 15 WDCS were convened. The groups rated 29 programmes across a range of provisions including pre-qualifying programmes (social work and mental health nursing), post-qualifying programmes, new graduate mental health worker programmes and programmes run within NHS Trusts. Overall, the results indicate that the majority of rated programmes are relevant to the policy agenda and involve service users in a meaningful way. However, courses are less likely to engage with carers and to assess the impact of the programmes. Key factors are identified that promote the implementation of the new quality assurance tool and key barriers to implementation are also elicited. The paper concludes that the tool can provide a useful framework to assess the quality of a broad range of mental health education, furthermore, that it should be incorporated into existing quality assurance systems.

Curriculum↗

PubMed2004

Teaching medical ethics: implementation and evaluation of a new course during residency training in bahrain.

AIM: This paper describes the development, implementation and evaluation of a new biomedical ethics course. The major educational goal was to enable the participants to critically analyse and resolve ethical dilemmas based on sound ethical and moral reasoning. BACKGROUND: The course was developed and implemented in the Family Practice Residency Program (FPRP) in the Kingdom of Bahrain. METHODOLOGY: Thirty-six family physician trainees participated in this course in May 2002 and January 2003. The curriculum was divided into five sessions, and each session had specific objectives, contents and teaching methods. The course was evaluated using pre- and post-tests, direct observation of participants and overall course assessment. RESULTS: Evaluations demonstrated that the participants scored higher in the post-test than in the pre-test. There was a significant statistical difference between the mean scores of both tests. After completing the course, participants produced more justifiable decisions than those generated at the beginning and felt more confident discussing and reasoning their decisions based on sound ethical and moral concepts. CONCLUSION: Our experience had demonstrated that the trainees benefited from a structured curriculum in biomedical ethics. We believe that the development and implementation of our course may serve as a case study for training and teaching postgraduates in the area of medical ethics.

Adult↗

PubMed2002

Smoking cessation in pregnancy: failure of an HMO pilot project to improve guideline implementation.

This pilot project investigated whether a system introduced by a health maintenance organization (HMO) could encourage obstetric providers to implement smoking-cessation guidelines in their offices. Staff from participating offices was trained in cessation counseling and paid $150 for each pregnant smoker counseled. Data were collected from chart review from participating physicians and a telephone survey of all HMO members giving birth before and after program implementation. Eighteen physician practices participated, representing 27 office sites and 80 physicians. Sixty-six staff members were trained in cessation counseling. Chart review revealed that identification of smoking status increased from 90% to 96% (p=0.03), but documentation of advice to quit worsened (62% vs. 24%, p=0.03). The HMO received claims for counseling from four pregnant smokers out of the 21 identified on chart review. The telephone survey revealed a similar prevalence of current smokers in the baseline and post-intervention samples (15% vs. 13%) but more former smokers (11% vs. 22%) in the follow-up. For the HMO as a whole, fewer smokers reported being advised to quit in the follow-up survey (86% vs. 65%). Few smokers reported being counseled to quit at baseline or follow-up (11% vs. 3%). None of the smokers who received obstetric care from a pilot group physician reported awareness of the smoking-cessation benefit despite the placement of brochures in participating offices advertising the program. This pilot project to reimburse for cessation counseling did not increase smoking-cessation advice or counseling in participating physician's offices. Smoking-cessation counseling worsened across the entire HMO obstetric community during the intervention. A more comprehensive systems approach and a larger HMO market share or a partnership among multiple HMOs may be required to increase smoking-cessation guideline implementation.

Adult↗

PubMed2006

Efficacy of safety-engineered device implementation in the prevention of percutaneous injuries: a review of published studies.

Nearly 6 years have passed since the Needlestick Safety and Prevention Act of 2000 was signed into law. We reviewed studies published since 1995 that evaluated the effect of safety-engineered device implementation on rates of percutaneous injury (PI) among health care workers. Criteria for inclusion of studies in the review were as follows: the intervention used to reduce PIs was a needleless system or a device with engineered sharps-injury protection, the outcome measurements included a PI rate, the intervention was evaluated in a defined population with clear comparison groups in clinical settings, and outcomes and denominators used for rate calculations were objectively measured using consistent methodology. All 17 studies reported substantial decreases in device-associated or overall PI rates after device implementation (range of reduction, 22%-100%). The majority of studies (n=12) were uncontrolled before-after trials with limited ability to control for confounding variables. In addition, implementation of safety-engineered devices was often accompanied by other interventions, and direct measurement of outcomes was not performed. Nevertheless, safety-engineered devices are an important component in PI prevention.

Equipment Safety↗

PubMed1999

Cost reduction with successful implementation of an antibiotic prophylaxis program in a private hospital in Ribeirão Preto, Brazil.

OBJECTIVE: To describe the implementation and results of a perioperative antibiotic prophylaxis (PAP) program. DESIGN: A protocol for correct use of PAP was implemented in December 1994. For selected months we measured the PAP protocol compliance of a random sample of clean and clean-contaminated procedures and calculated the cost of incorrect use of PAP. SELLING: A 180-bed general hospital in Ribeirão Preto, Brazil. RESULTS: The cost of unnecessary PAP in the obstetric and gynecologic, cardiothoracic, and orthopedic services dropped from $4,224.54 ($23.47/procedure) in November 1994 to $1,147.24 ($6.17/procedure, January 1995), $544.42 ($3.58/procedure, May 1995), $99.06 ($0.50/procedure, August 1995), and $30 ($0.12/procedure, March 1996). In November 1994, only 13.6% of all surgical procedures were done with correct use of PAP, compared to 59% in January 1995, 73% in August 1995, 78% in March 1996, 92% in November 1996, and 98% in May 1997. CONCLUSIONS: Incorrect PAP use wastes resources, which is a particular problem in developing countries. Our program is simple and can be implemented without the use of computers and now is being adopted in other hospitals in our region. We credit the success of our program to the commitment of all participants and to the strong support of the hospital directors.

Adult↗

PubMed2003

Implementation of the Canadian contingency plan for a case of suspected viral hemorrhagic fever.

OBJECTIVE: To describe the implementation of the Canadian contingency plan for viral hemorrhagic fever (VHF) in response to a suspected case. SETTING: A 300-bed, tertiary-care, university-affiliated hospital. PARTICIPANTS: A 32-year-old Congolese woman admitted to the hospital with suspected VHF in February 2001. Contact evaluation included hospital healthcare workers and laboratory staff. INTERVENTION: Enhanced isolation precautions were implemented in the patient care setting to prevent nosocomial transmission. Contact tracing and evaluation of close and high-risk contacts with symptoms was conducted. Laboratory precautions included barrier precautions and diversion of specimens. Communication occurred media. to both hospital employees and the media. RESULTS: Three high-risk contacts, 13 close contacts, and 60 casual contacts were identified. Two close contacts became symptomatic and required evaluation. Challenging process issues included tracing of laboratory specimens, decontamination of laboratory equipment, and internal and external communication. After 5 days, a transmissible VHF of public health consequence was ruled out in the index case. CONCLUSION: Contingency plans for VHF can be implemented in an efficient and feasible manner. Contact tracing, laboratory issues, internal communication, and media interest can be anticipated to be the key challenges.

Canada↗

PubMed2004

Prevention of infections associated with permanent cardiac antiarrhythmic devices by implementation of a comprehensive infection control program.

OBJECTIVE: To implement a comprehensive infection control (IC) program for prevention of cardiac device-associated infections (CDIs). DESIGN: Prospective before-after trial with 2 years of follow-up. SETTING: A tertiary-care, university-affiliated medical center. PATIENTS: A consecutive sample of all adults undergoing cardiac device implantation between 1997 and 2002. INTERVENTION: An IC program was implemented during late 2001 and included staff education, preoperative modification of patient risk factors, intraoperative control of strict aseptic technique, surgical scrubbing and attire, control of environmental risk factors, optimization of antibiotic prophylaxis, postoperative wound care, and active surveillance. The clinical endpoint was CDI rates. RESULTS: Between 1997 and 2000, there were 7 CDIs among 725 procedures (mean annual CDI incidence, 1%). During the first 9 months of 2001, there were 7 CDIs among 167 procedures (4.2%; P = .007): CDIs increased from 7 among 576 to 3 among 124 following pacemaker implantation (P = .39) and from 0 among 149 to 4 among 43 following cardioverter-defibrillator implantation (P = .002). Of the 14 CDIs, 5 involved superficial wounds, 7 involved deep wounds, and 2 involved endocarditis. Following intervention, there were no cases of CDI among 316 procedures during 24 months of follow-up (4.2% reduction; P = .0005). CONCLUSIONS: We observed a high CDI rate associated with substantial morbidity. IC measures had an impact on CDI. Although the relative weight of each measure in the prevention of CDI remains unknown, our results suggest that implementation of a comprehensive IC program is feasible and efficacious in this setting.

Adult↗

PubMed2004

Effect of implementing safety-engineered devices on percutaneous injury epidemiology.

OBJECTIVE: To assess the effect of implementing safety-engineered devices on percutaneous injury epidemiology, specifically on percutaneous injuries associated with a higher risk of blood-borne pathogen exposure. DESIGN: Before-and-after intervention trial comparing 3-year preintervention (1998--2000) and 1-year postintervention (2001--2002) periods. Percutaneous injury data have been entered prospectively into CDC NaSH software since 1998. SETTING: A 427-bed, tertiary-care hospital in Manhattan. PARTICIPANTS: All employees who reported percutaneous injuries during the study period. INTERVENTION: A "safer-needle system," composed of a variety of safety-engineered devices to allow for needle-safe IV delivery, blood collection, IV insertion, and intramuscular and subcutaneous injection, was implemented in February 2001. RESULTS: The mean annual incidence of percutaneous injuries decreased from 34.08 per 1,000 full-time-equivalent employees preintervention to 14.25 postintervention (P < .001). Reductions in the average monthly number of percutaneous injuries resulting from both low-risk (P < .01) and high-risk (P was not significant) activities were observed. Nurses experienced the greatest decrease (74.5%, P < .001), followed by ancillary staff (61.5%, P = .03). Significant rate reductions were observed for the following activities: manipulating patients or sharps (83.5%, P < .001), collisions or contact with sharps (73.0%, P = .01), disposal-related injuries (21.41%, P = .001), and catheter insertions (88.2%, P < .001). Injury rates involving hollow-bore needles also decreased (70.6%, P < .001). CONCLUSIONS: The implementation of safety-engineered devices reduced percutaneous injury rates across occupations, activities, times of injury, and devices. Moreover, intervention impact was observed when stratified by risk for blood-borne pathogen transmission.

Equipment Design↗

PubMed2004

Safety-engineered device implementation: does it introduce bias in percutaneous injury reporting?

OBJECTIVE: To examine whether implementation of safety-engineered devices in 2001 had an effect on rates of percutaneous injury (PI) reported by HCWs. DESIGN: Before-and-after intervention trial comparing 3-year preintervention (1998--2001) and 2-year postintervention (2001--2002) periods. PI data from anonymous, self-administered surveys were prospectively entered into CDC NaSH software. SETTING: A 427-bed, tertiary-care hospital in Manhattan. PARTICIPANTS: HCWs who attended state-mandated training sessions and completed the survey (1,132 preintervention; 821 postintervention). INTERVENTION: Implementation of a "safer-needle system" composed of various safety-engineered devices for needle-safe IV delivery-insertion, blood collection, and intramuscular-subcutaneous injection. RESULTS: Preintervention, the overall annual rate of PIs self-reported on the survey was 36.5 per 100 respondents, compared with 13.9 per 100 respondents postintervention (P < .01). The annual rate of formally reported PIs decreased from 8.3 to 3.1 per 100 respondents (P < .01). Report rates varied by occupational group (P < or = .02). The overall rate did not change between study periods (22.7% to 22.3%), although reporting improved among nurses (23.6% to 44.4%, P = .03) and worsened among building services staff (90.5% to 50%, P = .03). HCWs with greater numbers of PIs self-reported on the survey were less likely to formally report injuries (P < .01). The two most common reasons for nonreport (ie, thought injury was low risk or believed patient was low risk for blood-borne disease) did not vary from preintervention to postintervention. CONCLUSIONS: Safety-engineered device implementation decreased rates of PIs formally reported and self-reported on the survey. However, this intervention, with concomitant intensive education, had varying effects on reporting behavior by occupation and a minimal effect on overall reporting rates.

Bias↗

PubMed2006

Cluster of cases of severe acute respiratory syndrome among Toronto healthcare workers after implementation of infection control precautions: a case series.

OBJECTIVE: To review the severe acute respiratory syndrome (SARS) infection control practices, the types of exposure to patients with SARS, and the activities associated with treatment of such patients among healthcare workers (HCWs) who developed SARS in Toronto, Canada, after SARS-specific infection control precautions had been implemented. METHODS: A retrospective review of work logs and patient assignments, detailed review of medical records of patients with SARS, and comprehensive telephone-based interviews of HCWs who met the case definition for SARS after implementation of infection control precautions. RESULTS: Seventeen HCWs from 6 hospitals developed disease that met the case definition for SARS after implementation of infection control precautions. These HCWs had a mean age (+/-SD) of 39+/-2.3 years. Two HCWs were not interviewed because of illness. Of the remaining 15, only 9 (60%) reported that they had received formal infection control training. Thirteen HCWs (87%) were unsure of proper order in which personal protective equipment should be donned and doffed. Six HCWs (40%) reused items (eg, stethoscopes, goggles, and cleaning equipment) elsewhere on the ward after initial use in a room in which a patient with SARS was staying. Use of masks, gowns, gloves, and eyewear was inconsistent among HCWs. Eight (54%) reported that they were aware of a breach in infection control precautions. HCWs reported fatigue due to an increased number and length of shifts; participants worked a median of 10 shifts during the 10 days before onset of symptoms. Seven HCWs were involved in the intubation of a patient with SARS. One HCW died, and the remaining 16 recovered. CONCLUSION: Multiple factors were likely responsible for SARS in these HCWs, including the performance of high-risk patient care procedures, inconsistent use of personal protective equipment, fatigue, and lack of adequate infection control training.

Adult↗

PubMed1995

A method for implementing dynamic photon beam intensity modulation using independent jaws and a multileaf collimator.

A mathematical model is derived for digitally controlled linear accelerators to deliver a desired photon intensity distribution by combining collimator motion and machine dose rate variations. It shows that, at any instant, the quotient of the machine dose rate and the speed of collimator motion is proportional to the gradient of the desired in-air photon fluence distribution. The model is applicable for both independently controlled collimator jaws and multileaf collimators and can be implemented by controlling different parameters to accommodate linear accelerators from different manufactures. For independent jaws, each pair of jaws creates photon fluence variations along the direction of the jaw movement. For multileaf collimators, where each leaf is independently controlled, any two-dimensional (2D) photon fluence distribution can be delivered. The model has been implemented for wedged isodose distributions using independent jaws, and 2D intensity modulation using a multileaf collimator. One-dimensional (1D) wedged isodose distributions are created by moving an independent jaw at constant speed while varying machine dose rate. 2D intensity modulation has been implemented using a 'dynamic stepping' scheme, which controls the leaf progression during irradiation at constant machine dose rate. With this automated delivery scheme, the beam delivery time for dynamic intensity modulation, which depends on the complexity of the desired intensity distribution, approaches that of conventional beam modifiers. This paper shows the derivation of the model, its application, and our delivery scheme. Examples of 1D dynamic wedges and 2D intensity modulations will be given to illustrate the versatility of the model, the simplicity of its application, and the efficiency of beam delivery. These features make this approach practical for delivering conformal therapy treatments.

Biophysical Phenomena↗

PubMed2004

Implementation of outcome measures in a complementary and alternative medicine clinic: evidence of decreased pain and improved quality of life.

OBJECTIVES: The purpose of this study was twofold: (1) to design and implement a practical data collection system capable of obtaining pain and quality-of-life outcome measures in a complementary and alternative medicine (CAM) outpatient clinic and (2) to evaluate changes in patient status over time using these objective measures. DESIGN: A prospective study was carried out in an outpatient practice based setting. Scannable forms were designed utilizing Cardiff's TELEform system (Cardiff Software, Inc., Vista, CA) for data collection. SETTING/LOCATION: This study was conducted at Special Care Holistic Wellness Connection, an urban-based, hospital-affiliated, CAM clinic in Connecticut. SUBJECTS: Inclusion criteria consisted of: a starting pain level of 2 or more, subjects receiving 3 or more treatments in a specific modality, and a completed SF-12v2 Health Survey (Quality Metric Inc., Lincoln, RI). A total of 94 subjects were evaluated for acupuncture, chiropractic, or naturopathy. OUTCOME MEASURES: The Numeric Pain Analogue Scale and SF-12v2 Health Survey were used for subject evaluations and were compared from the first to the last treatments. International Classification of Disease codes were utilized to correlate and track the diagnosis. RESULTS: An outcome measures data management system was successfully implemented into a CAM outpatient clinical setting. Significant decreases in pain were observed in subjects receiving acupuncture, chiropractic, or naturopathy. In addition, improvements in various subscales of the SF-12v2 Physical and Mental Health categories were observed for each CAM treatment modality studied. CONCLUSIONS: This study established that a practical data collection system could be implemented in a CAM clinic utilizing several treatment modalities. In addition, outcome measures demonstrated both a significant reduction in pain and improvement in quality of life for subjects who utilized acupuncture, chiropractic, or naturopathy treatments.

Adult↗

PubMed1998

Implementation of a quality system (ISO 9000 series) for placental blood banking.

Although placental blood has recently become a new source of hematopoietic progenitors for marrow replacement, limited attention has been given to systems suitable to ensure the short-term and long-term quality of placental blood units used for transplantation. In this article, we describe a quality system for placental blood banking developed in accord with ISO 9002 norms at Milano Cord Blood Bank. The quality system is the organizational structure, procedures, processes, and resources needed to implement quality management. ISO 9002 is a model for quality assurance in production, installation, and servicing, which includes a number of clauses providing guidance for the implementation of the quality system. The quality system was started by the bank medical director with step 1: the general quality plan, which included (a) the written description of mission, objectives, technical and organizational policies, and staff organization chart of the placental blood bank, (b) the definition and acquisition of adequate financial, human, and structural resources, (c) the appointment of a quality system head independent from the production laboratory and reporting directly to the medical director. Tasks of the quality system head were (a) to identify the placental blood banking process together with the placental blood bank personnel, (b) to implement a documentation plan finalized at the production and maintenance of (i) the quality manual, which provides a summary on how the bank operates with a quality system in compliance with the ISO 9002 clauses, (ii) the general procedures (or quality system procedures), which provide more detail on selected clauses, including at least those prescribed by the ISO 9002 standard, (iii) the operative procedures (or process procedures), which describe in detail the process of placental blood banking and how technical activities must be performed, (iv) the work instructions, which provide stepwise descriptions of individual activities, (v) records/forms for data collection and storage, (c) to identify quality indicators, (d) to start a regular internal audit, (e) to report audit results to the medical director for review. This was followed by step 2: the job descriptions, staff training, and qualification; step 3: the documentation plan; step 4: the internal audit plan; step 5: the launch of the quality system, and step 6: the assessment by an external team from an accredited third-party organization and final certification for compliance to ISO 9002. The quality system, which must be maintained and undergo external audit at regular intervals so that certification is confirmed, ensures the high probability that placental blood units provided to clinicians conform regularly to predefined levels of quality.

Blood Banks↗

PubMed1997

Variation in training programmes for Resident Assessment Instrument implementation.

BACKGROUND: this paper provides an overview of the Minimum Data Set/Resident Assessment Instrument (MDS/RAI) training programmes in eight countries where the system has been introduced into nursing homes. Formal education and training in the skills of assessment and care planning of nursing home personnel is reputed to be poor. In response to this problem several researchers and clinicians view MDS/RAI implementation as an opportunity to upgrade staff knowledge in care of elderly people. RESULTS: the courses in the eight countries varied in content and length according to the different goals each interRAI researcher planned when the MDS/RAI was implemented. As expected the greatest differences in training approach were between the USA and other countries. In the USA, where the MDS/RAI was mandated for use in all nursing homes, tens of thousands of professionals had to be oriented to use the system in a relatively short period of time in order to comply with the law. The training programmes therefore tended to be very short compared with those that emerged in countries where the MDS/RAI was freely chosen and implemented.

Aged↗

PubMed1996

Implementing comprehensive pharmaceutical services at an academic tertiary care hospital.

The implementation and impact of comprehensive pharmaceutical services at a hospital are described. Before 1992, pharmaceutical services at Detroit Receiving Hospital and University Health Center were comparable to those of many departments serving similar academic tertiary care institutions. A major conflict with the principles of pharmaceutical care existed in that specific tasks were assigned to pharmacists, so that up to four pharmacists may have been involved in one patient's drug therapy while other patients were ignored. Several steps were taken to solve this problem. The department's mission and vision statements were modified to embrace pharmaceutical care. The support of administration and department leaders was secured, pharmacist evaluations were adjusted to make pharmaceutical care skills baseline competencies, and staffing was reconfigured. A voluntary pharmaceutical care committee was formed to transform pharmaceutical services at the hospital. It was decided that all staff pharmacists would provide clinical and distributive services on a rotating basis. The drug distribution system was altered to free more pharmacist time for patient care, and two technician positions were added. The clinical program was made more patient focused. The program was implemented in a stepwise manner beginning in September 1992. Computerized systems for tracking workload and documenting clinical interventions and drug cost savings were established. Later changes included making pharmacists responsible for all patients on a medical service rather than for specific problems in a particular location and changing scheduling to enhance the continuity of care. The number of clinical interventions by pharmacists increased from 3,563 in 1993 to 15,476 (projected) in 1995, and drug cost savings and avoidance increased from $239,248 in 1992 to $562,402 (projected) in 1995. Major change was necessary to implement comprehensive pharmaceutical services at an academic tertiary care hospital.

Cost Savings↗

PubMed1996

Work activities before and after implementation of an automated dispensing system.

The impact of an automated dispensing system (ADS) on medication-related work activities by nurses and pharmacists was studied. A point-of-care ADS (Baxter Sure-Med) was installed on two nursing units (the surgical intensive care unit [SICU] and a medicine unit [4NMU]) of a 400-bed university hospital as part of a pilot project. A self-reported work-sampling study was used to collect observations of medication-related work activities by nurses, health unit coordinators (nursing support staff), and pharmacists for a seven-day period before ADS implementation and a seven-day period after implementation. There were 7797 observations of nurse work activities, 1408 observations of health unit coordinator work activities, and 4236 observations of pharmacist work activities. The percentage of nurse work activities that were medication related decreased from 20.7% before ADS implementation to 18.4% afterward on 4NMU and increased slightly from 10.8% to 11.0% on the SICU. Medication-related health unit coordinator work activities increased from 17.5% to 25.3% of total activities on 4NMU and decreased from 16.6% to 10.7% on the SICU. None of these changes was significant. For decentralized pharmacists supporting 4NMU, the percentage of work activities classified as clinical increased significantly from 36.5% to 49.1%. For decentralized pharmacists supporting the SICU, clinical activities increased from 27.9% to 35.1%. There were no significant changes on either unit in pharmacist activities classified as technical. An overall measure of the efficiency with which pharmacists used their time for patient care-related activities increased. A point-of-care ADS did not affect the proportion of time spent by nurses on medication-related activities and seemed to give pharmacists more time for clinical work.

Automation↗

PubMed1992

Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system.

This paper reports our exploratory work to redesign, implement and integrate a collection of genome software tools with an object-oriented database system. Our software tools deal with genome data from Escherichia coli K-12, a bacterium that has been studied intensively and provides richer data sets than any other living organism. The object-oriented DBMS used for the integration is ONTOS, a commercial object-oriented system from Ontologic Inc. This redesign and implementation task was performed in two steps. First, C programs were converted into C++, and then the C++ version programs were modified and integrated with an object-oriented modeling of the data to form an ONTOS database application. The first step helps us develop a conceptual view for a DBMS-independent object-oriented construct. The second step elucidates what additional DBMS-dependent modification steps are needed to provide persistency to the objects. Examples are included to illustrate steps of the redesign and implementation. Overall, the outcome of this project demonstrates that programs and data can be successfully integrated with an object-oriented database, while providing the objects with persistency and shareability. This paper includes discussions using concrete examples on what advantage the object-oriented database approach provides over the relational database approach.

Base Sequence↗

PubMed2006

Clearcut: a fast implementation of relaxed neighbor joining.

SUMMARY: Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree reconstruction, it suffers from a O(N(3)) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N(2)logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation. AVAILABILITY: Clearcut source code is available for download at: http://bioinformatics.hungry.com/clearcut

Algorithms↗